SOLiD mapping with SHRiMP for genome with two different haplotype

Question

[saloebispo]

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

Answer 1

[brentp]

You can use bowtie1 which works fairly well for SOLiD (https://github.com/brentp/bowfast/tree/master/aligner-compare). Use the flag -m 1 to get only.