Hi everyone, I'm recently working on a batch of WGBS data, we are evaluating the sequencing outcome. We used BitMapperBS to align the reads, but …

Hi, I am currently looking through bam files using igv to manually check if the mutations not called by Mutect2 are really an error or …

I'm trying to retrieve the number of reads and the number of alignments with MAPQ=0. To address the question I'm using `samtools` in the following …

A year ago I started my bioinformatics learning from scratch and 0 background with unix systems. By then, I performed some alignment with tophat2 and …

<p>Hi,</p> <p>I have done variant calling on my file using <a href='http://samtools.sourceforge.net/'>samtools</a> mpile up and I have converetd my file from bcf to vcf. </p> …

<p>Hi everyone, I'm making a nice circo plot for my research and I'm having a trouble trying to plot axes for several stacked data tracks, …

<p>Hi,</p> <p>While analyzing some amplicons we decided to increase the mapping stringency in the post sequencing process to ensure the data was free of debris. …

<p>I am looking at mpileup output from RNA-Seq data, specifically at a location that looks like this.</p> <pre><code>&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&gt;&gt;&gt;&gt;&gt;&gt;&lt;&lt;&lt;&gt;&gt;&lt;&gt;&gt;&lt;&gt;&gt;&gt;&gt;&lt;&lt;&lt;&lt;&lt; G&gt;BB#GHJCCD#@#5#E;F##ICFEBIHDBDD;BB?IJGGGHJC##?EC </code></pre> <p>My understanding is that the …

<p>hi</p> <p>apologies if this is a trivial question.</p> <p>I've mapped SOLiD reads using BFAST and subsequently realigned the same with SRMA. There is considerably fewer …

<p>I recently read papers involving identifying disease-causing mutations using GATK for exome sequencing data. Most paper's pipeline is sth. like: </p> <pre><code>Call SNP/indel using GATK …