How to get the multiple matches of a same read in the results

[biobee07]

I will be very obliged if someone can help me with this question. I am new to the field of mapping reads with next gen sequencing.

I have Sanger reads 80-150 bp and I am using BWA to align my reads to the human genome. In the output of my results I get reads that are mapped to multiple locations, but the results have only one position returned (best hit). How do I get all the hits returned in my output.

Here are the parameters I have used:
bwa aln -n 0.10 -o 3 -M 1 -O 5 -E 1 /home/data/chr8_all.fa /home/data/data1.fastq > /home/data/data1_aln_sa.sai
bwa samse chr8_all.fa data1_aln_sa.sai data1.fastq > data1_aln.sam


Thanks
biobee

[dariober]

Hi biobee,

I think you have to look at the XA tag, which reports the alternative hits in the format chr, pos, CIGAR, NM. You can set the maximum number of hits to report with the -n option of samse.

Dario