SOLiD paired end reads mapping problems

Question

[MiguelMorard]

Hello,

I have Solid paired end reads (F3, F5) from DNA-Seq I want to map on a reference genome (yeast). I used Bowtie with the -C parameter and then I tried different values for the -v but I can't map more than 51% of the reads.

I would like to know if somebody uses other alignment tools with colorspace data that could perform better than bowtie.

Thanks a lot

Answer 1

[brentp]

That's solid data for you. Though 50% is pretty low. How long are the reads?

Back when I was subject to such horrible things, I did a comparison of various aligners on colorspace data https://github.com/brentp/bowfast/tree/master/aligner-compare

Bowtie should work well with the options here: https://github.com/brentp/bowfast/blob/master/aligner-compare/run-bowtie.sh

You can see that other aligners do better but they are more of a pain to deal with.

• bfast has huuuuge indexes
• shrimp requires splitting the data (but you can follow my run-shrimp.sh script
• novoalign isnt' free

sympathies.

[MiguelMorard]

The F3 are around 75bp and the F5 are around 35bp. I will try your parameters. I also found this yesterday but I haven't had time to test it.