BWA mapping colorspace reads

[Todd Scheetz]

Hi all,

Trying to map colorspace reads with BWA. According to my read of the manual page this should be possible, but have not successfully made it work.

I've built the color space index, but the alignment consistently fails.

have tried...
1) bwa aln -n5 -c index2/hg19c FILE
with FILE = CSFASTQ (solid2fastq from BFAST without -b option)
FILE = FASTQ (solid2fastq from BFAST with -b option)
Have also tried several other solid2fastq options (e.g. from BWA, Maq, etc)

Thanks,
Todd

[KevinLam]

how did it fail?
any errors?

this is how i did it

http://kevin-gattaca.blogspot.com/2010/08/howto-do-bwa-mapping-in-colorspace.html

[Todd Scheetz]

Hi Kevin,

Thanks for your reply. I tracked this down further and it turns out it was working, but the FASTQ files that were being generated by solid2fastq.pl were apparently of the "double-encoded" color space type. I had been comparing those to the sequence in the SAM output from a Bowtie analysis. Those did not match - but the SAM formatted output from the BWA analysis did match.

Your reply was very helpful in spurring me on to further investigate the results I did have. Given the apparent differences in the sequences I had convinced myself that there was something wrong with my approach. In reality I had followed those same steps exactly.

Thanks again!
Todd