Entering edit mode
9.0 years ago
saloebispo
•
0
I am work with a genome that has two haplotype (S and P), I need to map only one of them, or that reads go to only one of the genes of a particular haplotype.
SN:TcChr5-S LN:227319
@SQ SN:TcChr6-S LN:389024
@SQ SN:TcChr7-S LN:391095
@SQ SN:TcChr8-S LN:393423
@SQ SN:TcChr9-S LN:509634
@SQ SN:TcChr10-P LN:518846
@SQ SN:TcChr11-P LN:526141
@SQ SN:TcChr12-P LN:533093
@SQ SN:TcChr13-P LN:558364
I tried that best represents uniquely mapped reads. But doesn't work, someone has an idea, I looked in the manual but I found nothing very clear about it
SHRiMP_2_2_2/bin/gmapper-cs -N 5 --strata --single-best-mapping -o 1 solid_sample.csfasta genome.fasta >sample.sam