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gersteinlab / starrpeaker

STARRPeaker: STARR-seq peak caller
GNU General Public License v3.0
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samtools filter #4

Closed cxshine closed 4 years ago

cxshine commented 4 years ago

I have noticed that the preprocessing of pipeline is prepared for paired-end reads. But I have some data sets of single-end, and I also used bwa-mem to process them, does that make any difference? To filter alignments, which arguments of samtools should I choose?

hoondy commented 4 years ago

There shouldn't be any problem. I'd suggest using '--readstart' option if single-end is used. For samtools, a similar set of filters can be used, except anything related to 'mate' would be irrelevant.