SOLiD mapping with SHRiMP
1
0
Entering edit mode
6.7 years ago

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?

SOLiD SHRiMP • 1.7k views
ADD COMMENT
2
Entering edit mode
6.7 years ago

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

bowtie to the rescue! good stuff.

ADD REPLY

Login before adding your answer.

Traffic: 1523 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6