SOLiD mapping with SHRiMP

Question

[Damian Kao]

I am trying to find uniquely mapping SOLiD reads with SHRiMP. What parameters have you guys tried that best represents uniquely mapped reads?

It seems the --max-alignments option should be set to 1? What about the --strata or --single-best-mapping option?

Answer 1

[Istvan Albert]

I haven't used SOLiD data in a while and SHRiMP seems to not be actively developed anymore - I recall that bowtie 1 can also map color reads - customizing it might be easier.

[Damian Kao]

I haven't worked with SOLiD for a while either and I completely forgot about bowtie for cs mapping. Thanks. Ran it last night and it mapped 1.5billion reads in a couple of hours vs almost a day with SHRiMP.

[Istvan Albert]

bowtie to the rescue! good stuff.