Question: SOLiD mapping with SHRiMP
0
gravatar for Damian Kao
4.0 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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?

shrimp solid • 1.3k views
ADD COMMENTlink written 4.0 years ago by Damian Kao15k
2
gravatar for Istvan Albert
4.0 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Istvan Albert ♦♦ 79k

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.

ADD REPLYlink written 4.0 years ago by Damian Kao15k

bowtie to the rescue! good stuff.

ADD REPLYlink written 4.0 years ago by Istvan Albert ♦♦ 79k
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