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Creating conda environment for python2.7
TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on sp...2203 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumi...several tools. https://bioinformaticsonline.com/search?q=scaffolding&entity_type...bject&entity_subtype=bookmarks&offset=0&search_type=entities I could be w...2178 days ago
Learning Python Programming - a bioinformatician perspective !
Python Programming is a general purpose programming language that is open source,...need to be compiled. Interpreter parses the program code and generates the output. Py...he developers need to cast the type manually. Less code a...2196 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 -...2152 days ago
My commonly used commands in Bioinformatics
FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads....2124 days ago
Parallel Processing with Perl !
Here is a small tutorial on how to make best use of multiple processors for bioinforma...p;push (@childs,$fork); }elseif($fork==0){your code here;exit(0);}else{die &ldquo...creates a child process and takes the variables and code w...2093 days ago
- The benchmark module is a great tool to know the time the code takes to run. The output is usuall...ides us with a way to optimize our code. With the advent of petascale...rst_time = Benchmark->new; our code…… $second_time...the time taken by some part of the code i...
2093 days ago
- It's been a while since I last installed BLAT and when I went to...s now version 35 and that the code to download was: blatSrc...ecided to download the source code and compile that.I will be co...le that comes with the source code.One thing about building blat...or all architectures.The BLAT code a...
2076 days ago
- Follow this: Settings file Error Your web server does not have permission to create the settings.php...ur-user-id/public_html/elgg/elgg.1.8.0.1/ The directory where you put the Elgg code (...
906 days ago
Short-read assembly using Spades !
If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the...838 days ago
