**40**wrote:

Hi,

I am working with 454 data.

I am using BWA to mapping the reads onto the assembled contigs and I want to known all the possibilities.

I test that with samse and -n option is reliable if your input are short reads but not work with long reads (bwasw algorithm), Does someone known How can obtain multiple Hits (tag XA) using the bwasw algorithm?

EX: Test with short reads

```
bwa index -a is reference.fasta
bwa aln -N reference.fasta reads.fastq > aln_sa.sai
bwa samse -n 10 reference.fasta aln_sa.sai reads.fastq > aln.sam
less aln.sam
@SQ SN:gen_1 LN:910
@SQ SN:gen_2 LN:910
@SQ SN:gen_3 LN:910
@PG ID:bwa PN:bwa VN:0.5.9-r16
BCM10 0 gen_1 1 17 51M * 0 0
TTCATTACTTATTTGTAAAGCTTCTCTTTACAAAAGTCTCTTGTATTTTCC
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAIIIB5II+.9I$$ XT:A:U NM:i:0 X0:i:1
X1:i:4 XM:i:0 XO:i:0 XG:i:0 MD:Z:51
XA:Z:gen_2,+1,51M,2;gen_3,+1,51M,2;gen_1,+1,50M1S,2;gen_1,+1,51M,3;
BCM11 0 gen_1 71 20 51M * 0 0
GAGCAGTATTTTAAAATTCTGCCAATGGAGCTTAAGAGTGTTTATATCCGC
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII<IIII6III8@ XT:A:U NM:i:0 X0:i:1
X1:i:2 XM:i:0 XO:i:0 XG:i:0 MD:Z:51
XA:Z:gen_3,+71,51M,2;gen_2,+71,51M,2;
BCM14 0 gen_1 351 0 51M * 0 0
GCAATTGCATCATTGACCACAACAACAGATATGAACCTAGCGGCTGCCCAA
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIAIIIB5II+.9I$$ XT:A:R NM:i:0 X0:i:3
X1:i:6 XM:i:0 XO:i:0 XG:i:0 MD:Z:51
XA:Z:gen_3,+351,51M,0;gen_2,+351,51M,0;gen_1,+351,51M,3;gen_3,+351,51M,3;gen_2,+351,51M,3;gen_1,+351,50M1S,3;gen_3,+351,50M1S,3;gen_2,+351,50M1S,3;
```

**47k**• written 7.8 years ago by Cristina •

**40**