Mapping Paired End Solid Data Using Bwa
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10.2 years ago
Mahdi Sarmady ▴ 300

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 • 4.3k views
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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

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10.2 years ago
mylons ▴ 130

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

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7.9 years ago
brentp 23k

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.

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