This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Mapping Paired End Solid Data Using Bwa

Hi,

I need to map SOLiD paired end data with BWA. As it doesn't naturally support converting csfasta paired end (it supports mate pair), what is the best strategy to proceed?

I built color-space index of the reference. But converting csfasta to fastq does not work properly.

next-gen sequencing paired solid bwa
• 5,804 views • link
updated by brentp brentp • written by Mahdi Sarmady Mahdi Sarmady

@Mahdi: Can you guide me how you built the color-spaced index of genome? I am trying this: bwa index -a bwtsw -c GRCh38.r76.fa but I get the following error: index: invalid option -- 'c' . Can you guide me if this -c option is deprecated or what is wrong here. Thanks

• 1 views • link
written by Bioinformatist Newbie Bioinformatist Newbie

2 answers

I'd recommend trying bfast instead of bwa. It's more color space sensitive as the developer was hired by Life Technologies and asked to make tweaks to it supporting colorspace caveats.

Here's a good thread that outlines how to actually perform the analysis:
http://seqanswers.com/forums/showthread.php?t=7100

• 2 views • link
written by mylons mylons

A while back, I compared a lot of the aligners on colorspace using number of reads on target as a proxy for accuracy. You could use the commands from the scripts that I put here:

https://github.com/brentp/bowfast/tree/master/aligner-compare

BFAST does do very well, but it does take a while to run and the indexes are quite large.

• 0 views • link
written by brentp brentp

Log in to answer this question.

More posts like this