<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/43022?offset=10</link>
	<atom:link href="https://bioinformaticsonline.com/related/43022?offset=10" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26972/understanding-fastqc-output</guid>
	<pubDate>Fri, 15 Apr 2016 05:47:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26972/understanding-fastqc-output</link>
	<title><![CDATA[Understanding Fastqc Output]]></title>
	<description><![CDATA[<p>Understanding Following table and graphs</p>
<ol>
<li>Duplication level</li>
<li>kmer profile</li>
<li>per base GC content</li>
<li>per base N content</li>
<li>per base quality</li>
<li>per base sequence content</li>
<li>per sequence GC content</li>
<li>per sequence quality</li>
<li>sequence length distribution</li>
</ol>
<p>More at http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/</p><p>Address of the bookmark: <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/" rel="nofollow">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27238/slurm</guid>
	<pubDate>Wed, 04 May 2016 05:13:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27238/slurm</link>
	<title><![CDATA[SLURM]]></title>
	<description><![CDATA[<p><a href="http://www.schedmd.com/">SLURM</a> workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing.</p>
<p>This page is a <em>HOWTO</em> guide for setting up a <a href="http://www.schedmd.com/">SLURM</a> installation, currently focused on a CentOS 7 Linux OS. Please send feedback to Ole.H.Nielsen /at/ fysik.dtu.dk.</p>
<p>See the <a href="http://www.schedmd.com/">SLURM</a> homepage (also <a href="https://computing.llnl.gov/linux/slurm/">https://computing.llnl.gov/linux/slurm/</a>).</p><p>Address of the bookmark: <a href="https://wiki.fysik.dtu.dk/niflheim/SLURM" rel="nofollow">https://wiki.fysik.dtu.dk/niflheim/SLURM</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30093/velvet-tutorial</guid>
	<pubDate>Fri, 09 Dec 2016 04:19:07 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30093/velvet-tutorial</link>
	<title><![CDATA[Velvet tutorial]]></title>
	<description><![CDATA[<p><span>The objective of this activity is to help you understand how to run&nbsp;</span><a href="http://evomics.org/resources/software/genomics-software/assembly/velvet/" title="Velvet">Velvet</a><span>&nbsp;in general, how to accurately estimate the insert size of a paired-end library through the use of&nbsp;</span><a href="http://evomics.org/resources/software/genomics-software/assembly/bowtie/" title="Bowtie">Bowtie</a><span>, the primary parameters of velvet, and the process involved in producing a&nbsp;</span><em>de novo</em><span>&nbsp;assembly from Illumina reads.</span></p>
<p>http://evomics.org/learning/assembly-and-alignment/velvet/</p><p>Address of the bookmark: <a href="http://evomics.org/learning/assembly-and-alignment/velvet/" rel="nofollow">http://evomics.org/learning/assembly-and-alignment/velvet/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32399/mapping-ngs</guid>
	<pubDate>Tue, 02 May 2017 07:58:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32399/mapping-ngs</link>
	<title><![CDATA[Mapping NGS]]></title>
	<description><![CDATA[<p>NGS data are just a bunch of sequences, you have no idea which region in the genome each sequences comes from, which gene it represents...<br>To know that you have to align the sequences to the reference sequence. The reference sequence is in most cases the full genome sequence but sometimes, a library of EST sequences is used.<br>In either way, aligning your sequence reads to the reference sequence is called mapping.</p>
<p>The most used mappers of DNA-seq data are&nbsp;<a href="http://bio-bwa.sourceforge.net/" target="_blank">BWA</a>&nbsp;and&nbsp;<a href="http://bowtie-bio.sourceforge.net/bowtie2/index.shtml" target="_blank">Bowtie</a>&nbsp;for DNA-Seq data and&nbsp;<a href="http://tophat.cbcb.umd.edu/" target="_blank">Tophat</a>,&nbsp;<a href="https://github.com/alexdobin/STAR" target="_blank">STAR</a>&nbsp;or&nbsp;<a href="http://www.ccb.jhu.edu/software/hisat/index.shtml" target="_blank">HISAT</a>&nbsp;for RNA-Seq data. Mappers differ in which options they can take in, how fast and how accurate they are. Bowtie is faster than BWA, but looses some sensitivity (does not map an equal amount of reads to the correct position in the genome).</p><p>Address of the bookmark: <a href="http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data" rel="nofollow">http://wiki.bits.vib.be/index.php/Mapping_of_NGS_data</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44200/dashboard-designing-tutorial</guid>
	<pubDate>Thu, 02 Mar 2023 06:48:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44200/dashboard-designing-tutorial</link>
	<title><![CDATA[Dashboard designing tutorial !]]></title>
	<description><![CDATA[<p>Dashboard Design Tutorial</p><p>Address of the bookmark: <a href="https://github.com/dthill196/SARS-2-Dashboard-Tutorial" rel="nofollow">https://github.com/dthill196/SARS-2-Dashboard-Tutorial</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial</guid>
	<pubDate>Mon, 27 Nov 2017 16:24:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/34463/single-cell-rnaseq-data-analysis-tutorial</link>
	<title><![CDATA[Single Cell RNAseq data analysis tutorial !!]]></title>
	<description><![CDATA[<ul>
<li>A major breakthrough (replaced microarrays) in the late 00&rsquo;s and has been widely used since</li>
<li>Measures the&nbsp;average expression level&nbsp;for each gene across a large population of input cells</li>
<li>Useful for comparative transcriptomics, e.g.&nbsp;samples of the same tissue from different species</li>
<li>Useful for quantifying expression signatures from ensembles, e.g.&nbsp;in disease studies</li>
<li>Insufficient&nbsp;for studying heterogeneous systems, e.g.&nbsp;early development studies, complex tissues (brain)</li>
<li>Does&nbsp;not&nbsp;provide insights into the stochastic nature of gene expression</li>
</ul><p>Following are the useful links:</p><p><a href="http://hemberg-lab.github.io/scRNA.seq.course/scRNA-seq-course.pdf" target="_blank">Single Cell RNAseq data analysis Tutorial</a></p><p><a href="https://f1000research.com/articles/5-2122/v2" target="_blank">A step-by-step workflow for low-level analysis of single-cell RNA-seq data</a></p><p><a href="https://www.bioconductor.org/help/workflows/simpleSingleCell/" target="_blank">A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor</a></p><p>SCell: single-cell RNA-seq analysis software</p><p><a href="https://github.com/diazlab/SCell">https://github.com/diazlab/SCell</a></p><p>Beta-Poisson model for single-cell RNA-seq data analyses</p><p><a href="https://github.com/nghiavtr/BPSC">https://github.com/nghiavtr/BPSC</a></p><p>Sincera: A Computational Pipeline for Single Cell RNA-Seq Profiling Analysis</p><p><a href="https://research.cchmc.org/pbge/sincera.html">https://research.cchmc.org/pbge/sincera.html</a></p><p>SC3 &ndash; consensus clustering of single-cell RNA-Seq data</p><p><a href="http://biorxiv.org/content/early/2016/09/02/036558">http://biorxiv.org/content/early/2016/09/02/036558</a></p><p>Citrus: A toolkit for single cell sequencing analysis</p><p><a href="http://biorxiv.org/content/early/2016/09/14/045070">http://biorxiv.org/content/early/2016/09/14/045070</a></p><p>Single-Cell Resolution of Temporal Gene Expression during Heart Development</p><p><a href="http://www.cell.com/developmental-cell/fulltext/S1534-5807%2816%2930682-7">http://www.cell.com/developmental-cell/fulltext/S1534-5807(16)30682-7</a></p><p>Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects</p><p><a href="http://biorxiv.org/content/early/2016/11/15/087775">http://biorxiv.org/content/early/2016/11/15/087775</a></p><p>Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes</p><p><a href="http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract">http://genome.cshlp.org/content/early/2016/11/18/gr.212720.116.abstract</a></p><p>SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation</p><p><a href="http://biorxiv.org/content/early/2016/11/21/088856">http://biorxiv.org/content/early/2016/11/21/088856</a></p><p>SCOUP is a probabilistic model to analyze single-cell expression data during differentiation</p><p><a href="https://github.com/hmatsu1226/SCOUP">https://github.com/hmatsu1226/SCOUP</a></p><p>scLVM is a modelling framework for single-cell RNA-seq data</p><p><a href="https://github.com/PMBio/scLVM">https://github.com/PMBio/scLVM</a></p><p>Selective Locally linear Inference of Cellular Expression Relationships (SLICER) algorithm for inferring cell trajectories</p><p><a href="https://github.com/jw156605/SLICER">https://github.com/jw156605/SLICER</a></p><p>SinQC: A Method and Tool to Control Single-cell RNA-seq Data Quality</p><p><a href="http://www.morgridge.net/SinQC.html">http://www.morgridge.net/SinQC.html</a></p><p>TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis</p><p><a href="https://github.com/zji90/TSCAN">https://github.com/zji90/TSCAN</a></p><p>Visualization and cellular hierarchy inference of single-cell data using SPADE</p><p><a href="http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html">http://www.nature.com/nprot/journal/v11/n7/full/nprot.2016.066.html</a></p><p>OEFinder: Identify ordering effect genes in single cell RNA-seq data</p><p><a href="https://github.com/lengning/OEFinder">https://github.com/lengning/OEFinder</a></p>]]></description>
	<dc:creator>Robert M Willioms</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</guid>
	<pubDate>Fri, 26 Apr 2019 16:19:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</link>
	<title><![CDATA[AWK for beginners !]]></title>
	<description><![CDATA[<p>AWK is a standard tool on every POSIX-compliant UNIX system. It&rsquo;s like flex/lex, from the command-line, perfect for text-processing tasks and other scripting needs. It has a C-like syntax, but without mandatory semicolons (although, you should use them anyway, because they are required when you&rsquo;re writing one-liners, something AWK excels at), manual memory management, or static typing. It excels at text processing. You can call to it from a shell script, or you can use it as a stand-alone scripting language.</p><p>Why use AWK instead of Perl? Readability. AWK is easier to read than Perl. For simple text-processing scripts, particularly ones that read files line by line and split on delimiters, AWK is probably the right tool for the job.</p><div><pre><span>#!/usr/bin/awk -f</span>

<span># Comments are like this</span>


<span># AWK programs consist of a collection of patterns and actions.</span>
<span>pattern1</span> <span>{</span> <span>action</span><span>;</span> <span>}</span> <span># just like lex</span>
<span>pattern2</span> <span>{</span> <span>action</span><span>;</span> <span>}</span>

<span># There is an implied loop and AWK automatically reads and parses each</span>
<span># record of each file supplied. Each record is split by the FS delimiter,</span>
<span># which defaults to white-space (multiple spaces,tabs count as one)</span>
<span># You can assign FS either on the command line (-F C) or in your BEGIN</span>
<span># pattern</span>

<span># One of the special patterns is BEGIN. The BEGIN pattern is true</span>
<span># BEFORE any of the files are read. The END pattern is true after</span>
<span># an End-of-file from the last file (or standard-in if no files specified)</span>
<span># There is also an output field separator (OFS) that you can assign, which</span>
<span># defaults to a single space</span>

<span>BEGIN</span> <span>{</span>

    <span># BEGIN will run at the beginning of the program. It's where you put all</span>
    <span># the preliminary set-up code, before you process any text files. If you</span>
    <span># have no text files, then think of BEGIN as the main entry point.</span>

    <span># Variables are global. Just set them or use them, no need to declare..</span>
    <span>count</span> <span>=</span> <span>0</span><span>;</span>

    <span># Operators just like in C and friends</span>
    <span>a</span> <span>=</span> <span>count</span> <span>+</span> <span>1</span><span>;</span>
    <span>b</span> <span>=</span> <span>count</span> <span>-</span> <span>1</span><span>;</span>
    <span>c</span> <span>=</span> <span>count</span> <span>*</span> <span>1</span><span>;</span>
    <span>d</span> <span>=</span> <span>count</span> <span>/</span> <span>1</span><span>;</span> <span># integer division</span>
    <span>e</span> <span>=</span> <span>count</span> <span>%</span> <span>1</span><span>;</span> <span># modulus</span>
    <span>f</span> <span>=</span> <span>count</span> <span>^</span> <span>1</span><span>;</span> <span># exponentiation</span>

    <span>a</span> <span>+=</span> <span>1</span><span>;</span>
    <span>b</span> <span>-=</span> <span>1</span><span>;</span>
    <span>c</span> <span>*=</span> <span>1</span><span>;</span>
    <span>d</span> <span>/=</span> <span>1</span><span>;</span>
    <span>e</span> <span>%=</span> <span>1</span><span>;</span>
    <span>f</span> <span>^=</span> <span>1</span><span>;</span>

    <span># Incrementing and decrementing by one</span>
    <span>a</span><span>++</span><span>;</span>
    <span>b</span><span>--</span><span>;</span>

    <span># As a prefix operator, it returns the incremented value</span>
    <span>++</span><span>a</span><span>;</span>
    <span>--</span><span>b</span><span>;</span>

    <span># Notice, also, no punctuation such as semicolons to terminate statements</span>

    <span># Control statements</span>
    <span>if</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span>
        <span>print</span> <span>"Starting with count of 0"</span><span>;</span>
    <span>else</span>
        <span>print</span> <span>"Huh?"</span><span>;</span>

    <span># Or you could use the ternary operator</span>
    <span>print</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span> <span>?</span> <span>"Starting with count of 0"</span> <span>:</span> <span>"Huh?"</span><span>;</span>

    <span># Blocks consisting of multiple lines use braces</span>
    <span>while</span> <span>(</span><span>a</span> <span>&lt;</span> <span>10</span><span>)</span> <span>{</span>
        <span>print</span> <span>"String concatenation is done"</span> <span>" with a series"</span> <span>" of"</span>
            <span>" space-separated strings"</span><span>;</span>
        <span>print</span> <span>a</span><span>;</span>

        <span>a</span><span>++</span><span>;</span>
    <span>}</span>

    <span>for</span> <span>(</span><span>i</span> <span>=</span> <span>0</span><span>;</span> <span>i</span> <span>&lt;</span> <span>10</span><span>;</span> <span>i</span><span>++</span><span>)</span>
        <span>print</span> <span>"Good ol' for loop"</span><span>;</span>

    <span># As for comparisons, they're the standards:</span>
    <span># a &lt; b   # Less than</span>
    <span># a &lt;= b  # Less than or equal</span>
    <span># a != b  # Not equal</span>
    <span># a == b  # Equal</span>
    <span># a &gt; b   # Greater than</span>
    <span># a &gt;= b  # Greater than or equal</span>

    <span># Logical operators as well</span>
    <span># a &amp;&amp; b  # AND</span>
    <span># a || b  # OR</span>

    <span># In addition, there's the super useful regular expression match</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>
    <span>if</span> <span>(</span><span>"boo"</span> <span>!~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Boo!"</span><span>;</span>

    <span># Arrays</span>
    <span>arr</span><span>[</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>arr</span><span>[</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>

    <span># You can also initialize an array with the built-in function split()</span>

    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo:bar:baz"</span><span>,</span> <span>arr</span><span>,</span> <span>":"</span><span>);</span>

    <span># You also have associative arrays (actually, they're all associative arrays)</span>
    <span>assoc</span><span>[</span><span>"foo"</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>assoc</span><span>[</span><span>"bar"</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>

    <span># And multi-dimensional arrays, with some limitations I won't mention here</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"boo"</span><span>;</span>

    <span># You can test for array membership</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>

    <span># You can also use the 'in' operator to traverse the keys of an array</span>
    <span>for</span> <span>(</span><span>key</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>assoc</span><span>[</span><span>key</span><span>];</span>

    <span># The command line is in a special array called ARGV</span>
    <span>for</span> <span>(</span><span>argnum</span> <span>in</span> <span>ARGV</span><span>)</span>
        <span>print</span> <span>ARGV</span><span>[</span><span>argnum</span><span>];</span>

    <span># You can remove elements of an array</span>
    <span># This is particularly useful to prevent AWK from assuming the arguments</span>
    <span># are files for it to process</span>
    <span>delete</span> <span>ARGV</span><span>[</span><span>1</span><span>];</span>

    <span># The number of command line arguments is in a variable called ARGC</span>
    <span>print</span> <span>ARGC</span><span>;</span>

    <span># AWK has several built-in functions. They fall into three categories. I'll</span>
    <span># demonstrate each of them in their own functions, defined later.</span>

    <span>return_value</span> <span>=</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>);</span>
    <span>string_functions</span><span>();</span>
    <span>io_functions</span><span>();</span>
<span>}</span>

<span># Here's how you define a function</span>
<span>function</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>,</span>     <span>d</span><span>)</span> <span>{</span>

    <span># Probably the most annoying part of AWK is that there are no local</span>
    <span># variables. Everything is global. For short scripts, this is fine, even</span>
    <span># useful, but for longer scripts, this can be a problem.</span>

    <span># There is a work-around (ahem, hack). Function arguments are local to the</span>
    <span># function, and AWK allows you to define more function arguments than it</span>
    <span># needs. So just stick local variable in the function declaration, like I</span>
    <span># did above. As a convention, stick in some extra whitespace to distinguish</span>
    <span># between actual function parameters and local variables. In this example,</span>
    <span># a, b, and c are actual parameters, while d is merely a local variable.</span>

    <span># Now, to demonstrate the arithmetic functions</span>

    <span># Most AWK implementations have some standard trig functions</span>
    <span>localvar</span> <span>=</span> <span>sin</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>cos</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>atan2</span><span>(</span><span>b</span><span>,</span> <span>a</span><span>);</span> <span># arc tangent of b / a</span>

    <span># And logarithmic stuff</span>
    <span>localvar</span> <span>=</span> <span>exp</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>log</span><span>(</span><span>a</span><span>);</span>

    <span># Square root</span>
    <span>localvar</span> <span>=</span> <span>sqrt</span><span>(</span><span>a</span><span>);</span>

    <span># Truncate floating point to integer</span>
    <span>localvar</span> <span>=</span> <span>int</span><span>(</span><span>5.34</span><span>);</span> <span># localvar =&gt; 5</span>

    <span># Random numbers</span>
    <span>srand</span><span>();</span> <span># Supply a seed as an argument. By default, it uses the time of day</span>
    <span>localvar</span> <span>=</span> <span>rand</span><span>();</span> <span># Random number between 0 and 1.</span>

    <span># Here's how to return a value</span>
    <span>return</span> <span>localvar</span><span>;</span>
<span>}</span>

<span>function</span> <span>string_functions</span><span>(</span>    <span>localvar</span><span>,</span> <span>arr</span><span>)</span> <span>{</span>

    <span># AWK, being a string-processing language, has several string-related</span>
    <span># functions, many of which rely heavily on regular expressions.</span>

    <span># Search and replace, first instance (sub) or all instances (gsub)</span>
    <span># Both return number of matches replaced</span>
    <span>localvar</span> <span>=</span> <span>"fooooobar"</span><span>;</span>
    <span>sub</span><span>(</span><span>"fo+"</span><span>,</span> <span>"Meet me at the "</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "Meet me at the bar"</span>
    <span>gsub</span><span>(</span><span>"e+"</span><span>,</span> <span>"."</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "m..t m. at th. bar"</span>

    <span># Search for a string that matches a regular expression</span>
    <span># index() does the same thing, but doesn't allow a regular expression</span>
    <span>match</span><span>(</span><span>localvar</span><span>,</span> <span>"t"</span><span>);</span> <span># =&gt; 4, since the 't' is the fourth character</span>

    <span># Split on a delimiter</span>
    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo-bar-baz"</span><span>,</span> <span>arr</span><span>,</span> <span>"-"</span><span>);</span> <span># a[1] = "foo"; a[2] = "bar"; a[3] = "baz"; n = 3</span>

    <span># Other useful stuff</span>
    <span>sprintf</span><span>(</span><span>"%s %d %d %d"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "Testing 1 2 3"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "oob"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>4</span><span>);</span> <span># =&gt; "bar"</span>
    <span>length</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; 3</span>
    <span>tolower</span><span>(</span><span>"FOO"</span><span>);</span> <span># =&gt; "foo"</span>
    <span>toupper</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; "FOO"</span>
<span>}</span>

<span>function</span> <span>io_functions</span><span>(</span>    <span>localvar</span><span>)</span> <span>{</span>

    <span># You've already seen print</span>
    <span>print</span> <span>"Hello world"</span><span>;</span>

    <span># There's also printf</span>
    <span>printf</span><span>(</span><span>"%s %d %d %d\n"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span>

    <span># AWK doesn't have file handles, per se. It will automatically open a file</span>
    <span># handle for you when you use something that needs one. The string you used</span>
    <span># for this can be treated as a file handle, for purposes of I/O. This makes</span>
    <span># it feel sort of like shell scripting, but to get the same output, the string</span>
    <span># must match exactly, so use a variable:</span>

    <span>outfile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>

    <span>print</span> <span>"foobar"</span> <span>&gt;</span> <span>outfile</span><span>;</span>

    <span># Now the string outfile is a file handle. You can close it:</span>
    <span>close</span><span>(</span><span>outfile</span><span>);</span>

    <span># Here's how you run something in the shell</span>
    <span>system</span><span>(</span><span>"echo foobar"</span><span>);</span> <span># =&gt; prints foobar</span>

    <span># Reads a line from standard input and stores in localvar</span>
    <span>getline</span> <span>localvar</span><span>;</span>

    <span># Reads a line from a pipe (again, use a string so you close it properly)</span>
    <span>cmd</span> <span>=</span> <span>"echo foobar"</span><span>;</span>
    <span>cmd</span> <span>|</span> <span>getline</span> <span>localvar</span><span>;</span> <span># localvar =&gt; "foobar"</span>
    <span>close</span><span>(</span><span>cmd</span><span>);</span>

    <span># Reads a line from a file and stores in localvar</span>
    <span>infile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>
    <span>getline</span> <span>localvar</span> <span>&lt;</span> <span>infile</span><span>;</span> 
    <span>close</span><span>(</span><span>infile</span><span>);</span>
<span>}</span>

<span># As I said at the beginning, AWK programs consist of a collection of patterns</span>
<span># and actions. You've already seen the BEGIN pattern. Other</span>
<span># patterns are used only if you're processing lines from files or standard</span>
<span># input.</span>
<span>#</span>
<span># When you pass arguments to AWK, they are treated as file names to process.</span>
<span># It will process them all, in order. Think of it like an implicit for loop,</span>
<span># iterating over the lines in these files. these patterns and actions are like</span>
<span># switch statements inside the loop. </span>

<span>/^fo+bar$/</span> <span>{</span>

    <span># This action will execute for every line that matches the regular</span>
    <span># expression, /^fo+bar$/, and will be skipped for any line that fails to</span>
    <span># match it. Let's just print the line:</span>

    <span>print</span><span>;</span>

    <span># Whoa, no argument! That's because print has a default argument: $0.</span>
    <span># $0 is the name of the current line being processed. It is created</span>
    <span># automatically for you.</span>

    <span># You can probably guess there are other $ variables. Every line is</span>
    <span># implicitly split before every action is called, much like the shell</span>
    <span># does. And, like the shell, each field can be access with a dollar sign</span>

    <span># This will print the second and fourth fields in the line</span>
    <span>print</span> <span>$</span><span>2</span><span>,</span> <span>$</span><span>4</span><span>;</span>

    <span># AWK automatically defines many other variables to help you inspect and</span>
    <span># process each line. The most important one is NF</span>

    <span># Prints the number of fields on this line</span>
    <span>print</span> <span>NF</span><span>;</span>

    <span># Print the last field on this line</span>
    <span>print</span> <span>$</span><span>NF</span><span>;</span>
<span>}</span>

<span># Every pattern is actually a true/false test. The regular expression in the</span>
<span># last pattern is also a true/false test, but part of it was hidden. If you</span>
<span># don't give it a string to test, it will assume $0, the line that it's</span>
<span># currently processing. Thus, the complete version of it is this:</span>

<span>$</span><span>0</span> <span>~</span> <span>/^fo+bar$/</span> <span>{</span>
    <span>print</span> <span>"Equivalent to the last pattern"</span><span>;</span>
<span>}</span>

<span>a</span> <span>&gt;</span> <span>0</span> <span>{</span>
    <span># This will execute once for each line, as long as a is positive</span>
<span>}</span>

<span># You get the idea. Processing text files, reading in a line at a time, and</span>
<span># doing something with it, particularly splitting on a delimiter, is so common</span>
<span># in UNIX that AWK is a scripting language that does all of it for you, without</span>
<span># you needing to ask. All you have to do is write the patterns and actions</span>
<span># based on what you expect of the input, and what you want to do with it.</span>

<span># Here's a quick example of a simple script, the sort of thing AWK is perfect</span>
<span># for. It will read a name from standard input and then will print the average</span>
<span># age of everyone with that first name. Let's say you supply as an argument the</span>
<span># name of a this data file:</span>
<span>#</span>
<span># Bob Jones 32</span>
<span># Jane Doe 22</span>
<span># Steve Stevens 83</span>
<span># Bob Smith 29</span>
<span># Bob Barker 72</span>
<span>#</span>
<span># Here's the script:</span>

<span>BEGIN</span> <span>{</span>

    <span># First, ask the user for the name</span>
    <span>print</span> <span>"What name would you like the average age for?"</span><span>;</span>

    <span># Get a line from standard input, not from files on the command line</span>
    <span>getline</span> <span>name</span> <span>&lt;</span> <span>"/dev/stdin"</span><span>;</span>
<span>}</span>

<span># Now, match every line whose first field is the given name</span>
<span>$</span><span>1</span> <span>==</span> <span>name</span> <span>{</span>

    <span># Inside here, we have access to a number of useful variables, already</span>
    <span># pre-loaded for us:</span>
    <span># $0 is the entire line</span>
    <span># $3 is the third field, the age, which is what we're interested in here</span>
    <span># NF is the number of fields, which should be 3</span>
    <span># NR is the number of records (lines) seen so far</span>
    <span># FILENAME is the name of the file being processed</span>
    <span># FS is the field separator being used, which is " " here</span>
    <span># ...etc. There are plenty more, documented in the man page.</span>

    <span># Keep track of a running total and how many lines matched</span>
    <span>sum</span> <span>+=</span> <span>$</span><span>3</span><span>;</span>
    <span>nlines</span><span>++</span><span>;</span>
<span>}</span>

<span># Another special pattern is called END. It will run after processing all the</span>
<span># text files. Unlike BEGIN, it will only run if you've given it input to</span>
<span># process. It will run after all the files have been read and processed</span>
<span># according to the rules and actions you've provided. The purpose of it is</span>
<span># usually to output some kind of final report, or do something with the</span>
<span># aggregate of the data you've accumulated over the course of the script.</span>

<span>END</span> <span>{</span>
    <span>if</span> <span>(</span><span>nlines</span><span>)</span>
        <span>print</span> <span>"The average age for "</span> <span>name</span> <span>" is "</span> <span>sum</span> <span>/</span> <span>nlines</span><span>;</span>
<span>}</span>
</pre><p><span>&nbsp;</span></p></div>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems</guid>
	<pubDate>Sat, 26 Jun 2021 15:37:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems</link>
	<title><![CDATA[Calling variants in non-diploid systems]]></title>
	<description><![CDATA[<p><span>The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial&nbsp;</span><span>DNA</span><span>&nbsp;although the same approaches will work equally good on viral and bacterial genomes (</span><a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#Rebolledo-Jaramillo2014">Rebolledo-Jaramillo&nbsp;<em>et al.</em>&nbsp;2014</a><span>,&nbsp;</span><a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#Li2015">Li&nbsp;<em>et al.</em>&nbsp;2015</a><span>).</span></p><p>Address of the bookmark: <a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html" rel="nofollow">https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38212/megahit-an-ultra-fast-single-node-solution-for-large-and-complex-metagenomics-assembly-via-succinct-de-bruijn-graph</guid>
	<pubDate>Wed, 14 Nov 2018 04:50:27 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38212/megahit-an-ultra-fast-single-node-solution-for-large-and-complex-metagenomics-assembly-via-succinct-de-bruijn-graph</link>
	<title><![CDATA[MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph]]></title>
	<description><![CDATA[<p><span>MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct&nbsp;</span><em>de Bruijn</em><span>&nbsp;graph (SdBG) to achieve low memory assembly. MEGAHIT can&nbsp;</span><span>optionally</span><span>&nbsp;utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.</span></p>
<p><span>https://academic.oup.com/bioinformatics/article/31/10/1674/177884</span></p><p>Address of the bookmark: <a href="https://github.com/voutcn/megahit" rel="nofollow">https://github.com/voutcn/megahit</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures</guid>
	<pubDate>Thu, 04 Jun 2020 23:19:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41825/hnadock-a-nucleic-acid-docking-server-for-modeling-rnadna%E2%80%93rnadna-3d-complex-structures</link>
	<title><![CDATA[HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures]]></title>
	<description><![CDATA[<p><span>The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users are required to provide the three-dimensional (3D) structures of the two molecules to be docked.&nbsp;</span></p><p>Address of the bookmark: <a href="http://huanglab.phys.hust.edu.cn/hnadock/" rel="nofollow">http://huanglab.phys.hust.edu.cn/hnadock/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>

</channel>
</rss>