Question

Mapping Paired End Solid Data Using Bwa

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13.3 years ago

Mahdi Sarmady ▴ 310

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 • 5.2k views

ADD COMMENT • link updated 11.0 years ago by brentp 24k • written 13.3 years ago by Mahdi Sarmady ▴ 310

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@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

ADD REPLY • link 8.4 years ago by Bioinformatist Newbie ▴ 270

score 5 · Answer 1 · 2011-08-13

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

score 0 · Answer 2 · 2013-12-03

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.