Results for "output"
Blogs
How to install Perl modules manually, using CPAN command, and other quick ways
...e are now dependent all these tiny magicians :). # yum install perl-CPANOutput of yum install perl-CPAN comm...BioPerl in your server/computer. # sudo apt-cache search perl BioPerl Output will be like as follows: bio...3942 days ago
Five unique traits of effective computational biologist
...o my supervisor most of the computational biologist, don't know what they are doing biologically. Even they struggle to explain their own programs output and results. Therefore, It is...3943 days ago
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Bookmarks
Public Databases for Bioinformatics !
...o = multiprocessing.Queue() for i in xrange(NSIMS): todo.put(i) for i in xrange(NPROC): todo.put('FINISHED') ofp = ProcessSafeOPStream( open("output.txt", "w") ) pids = [] fo...1132 days ago
- ...CuffDiff* EdgeR* DESeq2 Advanced Command Line Tutorial Graphical Output with CummeRbund introduces so...PC (explained in the Tutorial). You will learn how to produce graphical output from RNA-Seq analysis previou...
3645 days ago
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Files
- Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3859 days ago
Pages
Check the Size of a directory & Free disk space.
...s in kilobytes (default). The last line of the output gives you the total size of t...dquo;command with some flag gives you a better output than the default one. The opt...ives you a grand total as the last line of the output. So if your directory occupie...3695 days ago
A guide for complete R beginners :- Getting data into R
...s in an object at any time by typing its name; x will produce the output ‘[1] 1 2 3 4 5′...ount of Something”) Note Nothing will appear on screen, the output is going to the file Also it...3350 days ago
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Top-level pages
Most Commonly used Awk by Bioinformatician
...where column 3 is larger than column 5: awk '$3>$5' input.txt > output.txt extract column 2,4,5: awk '{print $2,$4,$5}' input.txt > output.txt awk 'BEGIN{OFS="\t"}{pri...3905 days ago
List of In-silico Binding Site Prediction Tools
...protein-binding sites defined by interactions with small molecules. The output is a detailed list of the sha...e input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the sha...3736 days ago
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Wire posts
News
- ...re are several BLAST parsers are available, but they are often missing some important features, such as keeping all information from the raw BLAST output, allowing direct access to si...
3882 days ago
- ...el.get_deletions() and model.loops() now have an include_termini option; if False, residue ranges that include chain termini are excluded from the output. See the Modeller manual for...
3726 days ago
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Opportunity posts
Research fellow (PhD candidate) in computational biology – 2 positions
...ll analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will...3655 days ago
Post-Doc Positions at the Institute of Evolution, University of Haifa, Haifa, Israel
...y, for Post-Docs experts in bioinformatics with a background of good understanding biological questions. That is that can independently handle raw output data of RNA-seq / miR seq/ Ge...3524 days ago
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Video
Bioinformatics 101 - Running BLAST
How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered live at the Tomato Disease Worksho...3889 days ago
Bio-Scripts
R script to visualize fastANI core-genome comparison
...ose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR packa...visual_file=commandArgs(TRUE)[3] library(genoPlotR) #Read fastANI output comparison...1094 days ago
- ...irectory of sequences $myDir = "/home/anjana/seqs"; # Output directory (relative to $myDir or full path) $outputDir = "OutDir"; # Path to p...as per their need print "$patFile \t$seqFile \t $outputDir/$outFile\n"; } }
2908 days ago
- +52 more Bio-Scripts
Tryst
Tryst with a Bioinformatician # Dr Altan Kara
...run by only looking at the results instead of just blindly trusting the output of the bioinformatics tools....nmental control. In other words, one should always easily control input output directories, modify files or...2354 days ago
Tags
Converting BLAST output into CSV
Suppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific format. If the program is popular enough, there w...Tags: Convert, BLAST, output, CSV, blastn, megablast
2330 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident length mismatch gapopen qstart qend sstart send eva...Tags: BLASTn, blast, alignment, output, format, 6
2131 days ago
Comments
Comment on "Benchmarking Perl Module !"
...k for 100 iterations: timethese(100, { 'MyModule' => \&benchmark_my_module, }); Analyze the results: The timethese function will output the results of the benchmark,...408 days ago
Comment on "Short-read assembly using Spades !"
...ce. The command for running SPAdes is usually as follows: spades.py -o output_directory -1 forward_reads.fastq -2 reverse_reads.fastq Here, "output_directory" is the name of the...408 days ago
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