I am having trouble with the -n option with bwa samse (version 0.5.3). If I either leave it off or use -n -1, I do get apparently good results in SAM format. But if I put any positive number in, I get something else. It looked like this for one case:
>081017-and-081020:1:1:1715:1759 1 1
PHIX174 -322 2
Could anyone tell me what's going on here? I was expecting SAM output. How are we supposed to use this output?
UPDATE:
I looked again at the manual and this time I noticed the following:
When -n is applied, multiple positions will be printed in a concise format. The ‘>’ line in the output shows the read name, the number of printed hits and the number of stored hits; the following lines give the chromosomal coordinates and the edit distance.
So, that clears up what the output is. Basically, if I understand things, it is impossible to get multiple hit output in SAM format? Is this a limitation of SAM, or something else?
>081017-and-081020:1:1:1715:1759 1 1
PHIX174 -322 2
Could anyone tell me what's going on here? I was expecting SAM output. How are we supposed to use this output?
UPDATE:
I looked again at the manual and this time I noticed the following:
When -n is applied, multiple positions will be printed in a concise format. The ‘>’ line in the output shows the read name, the number of printed hits and the number of stored hits; the following lines give the chromosomal coordinates and the edit distance.
So, that clears up what the output is. Basically, if I understand things, it is impossible to get multiple hit output in SAM format? Is this a limitation of SAM, or something else?