I am running a snakemake pipeline, and I had two reference genomes. One with fasta extension, and the other without. I also had two rules …

Apologies if this is a simple question, but I was trying to find a centralized biological knowledge graph (ie. connecting genes/proteins/actions/lipids/diseases, etc.) but I couldn't …

Hi, I have a very fragmented reference genome https://www.g3journal.org/content/9/7/2039 samtool generate a huge fai index file of 1.35gb, which is way too big to load …

I'm trying to learn the theory behind various steps in variant calling using GATK. Before alignment using BWA-MEM we first index the reference genome and …

I would like to generate a .fai file for all the snps belonging to a specific gene. How I'll be able to do that? Do …

<p>Do the sequences in <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a>/BAM header have to match the number and the order of the sequences in reference FASTA file?</p> <p>For example, if …

How does the [GenomeBrowse][1] genome browser from Golden Helix compare to IGV? What are the pros and cons? [1]: http://www.goldenhelix.com/GenomeBrowse/

<p>I am new to bioinformatics and I have a long drive to work.</p> <p>What are some good audio resources for bioinformatics? For example:</p> <ul> <li>full …

<p>The SAM specification states that <code>@RG-&gt;SM</code> is:</p> <pre><code>Sample. Use pool name where a pool is being sequenced. </code></pre> <p>"sample" is a general word. What is …

<p>Here is what the <a href="http://samtools.sourceforge.net/samtools.shtml">docs</a> say:</p> <blockquote> <p>-t FILE This file is TAB-delimited. Each line must contain the reference name and the length of …