<p>I am mapping some RNA-seq data with <a href='http://bio-bwa.sourceforge.net/'>bwa</a> and would like to do some analysis on where multi-mapped reads fall.</p> <p>I know that I …
<p>I would like to know more about how <a href='http://bio-bwa.sourceforge.net/'>BWA</a> treats the mapping score of paired end reads. </p> <p>I am familiar with the process …
<p>My output of <a href='http://bio-bwa.sourceforge.net/'>BWA</a> index has only 4 files as </p> <p>mm10.fa.amb mm10.fa.ann mm10.fa.bwt mm10.fq.pac</p> <p>I read a thread that a guy's <a href='http://bio-bwa.sourceforge.net/'>BWA</a> …
<p>When I use new version <a href='http://bio-bwa.sourceforge.net/'>BWA</a> 0.7.5a to align my 78bp pair-end reads with reference genome under Linux, Index the genome and generate alignments …
<p>I am the first to install <a href='http://bio-bwa.sourceforge.net/'>BWA</a> and never use this software by commands of Linux.When I try to install <a href='http://bio-bwa.sourceforge.net/'>BWA</a> under <a …
<p>I am looking for a description of <a href='http://bio-bwa.sourceforge.net/'>bwa</a> algorithm for mapping with gaps. More precisely I wonder how <a href='http://bio-bwa.sourceforge.net/'>bwa</a> handles mismatches in reads …
<p>According to <a href='http://www.nature.com/jhg/journal/vaop/ncurrent/full/jhg201143a.html'>this</a> article in the Journal of Human Genetics (Apr-28, 2011), Bowtie jut doesn't work with pair end reads. For details, see table …