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Hi,
I downloaded an sra file of whole exome seq.
When trying to convert it to a sam file I use the -u flag to get the unaligned reads. However, when I compare this to a run without the -u flag I see the exact same reads.
The only difference is that without the -u the reads for which there is no aligned match (i.e. $7==*) have a flag field of 0 (i.e. $2==0).
When I run with -u the flag field gets a value.
Also, of course, the unaligned pair is not in the file.
Is this a bug?
I downloaded an sra file of whole exome seq.
When trying to convert it to a sam file I use the -u flag to get the unaligned reads. However, when I compare this to a run without the -u flag I see the exact same reads.
The only difference is that without the -u the reads for which there is no aligned match (i.e. $7==*) have a flag field of 0 (i.e. $2==0).
When I run with -u the flag field gets a value.
Also, of course, the unaligned pair is not in the file.
Is this a bug?