Question: SOLiD paired end reads mapping problems
gravatar for MiguelMorard
4.2 years ago by
MiguelMorard20 wrote:


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

dna bowtie sequence alignment solid • 1.6k views
ADD COMMENTlink modified 4.2 years ago by brentp22k • written 4.2 years ago by MiguelMorard20
gravatar for brentp
4.2 years ago by
Salt Lake City, UT
brentp22k wrote:

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


Bowtie should work well with the options here:

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 script
  • novoalign isnt' free



ADD COMMENTlink written 4.2 years ago by brentp22k

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.


ADD REPLYlink written 4.2 years ago by MiguelMorard20
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