BWA results without coordinates

[Francesco Lescai]

Dear all,
I am a beginner and I'm starting to use BWA in a small resequencing project: one single gene, with a high coverage.

I obtained some odds results from BWA: the final .sam fine does not have chromosome coordinates. Both values (where the chromosome and its position should appear) are set to zero.

I do not get any error in the three steps (index/aln/samse).
I tried both the bwt-sw method as well as the IS one for the indexing step, as my reference is a single chromosome where the gene is located.
They both give the same end results without coordinates.

Has anyone a clue, or experienced the same problem?

thanks!

[nilshomer]

Dear all,
I am a beginner and I'm starting to use BWA in a small resequencing project: one single gene, with a high coverage.

I obtained some odds results from BWA: the final .sam fine does not have chromosome coordinates. Both values (where the chromosome and its position should appear) are set to zero.

I do not get any error in the three steps (index/aln/samse).
I tried both the bwt-sw method as well as the IS one for the indexing step, as my reference is a single chromosome where the gene is located.
They both give the same end results without coordinates.

Has anyone a clue, or experienced the same problem?

thanks!

It's not a problem, it's a feature (unmapped reads)! Please read to the SAM specification carefully.

[Francesco Lescai]

Thank you for the quick answer. I understand this.
But I run the analysis in MAQ and most of the reads are correctly mapped.
So why BWA doesn't map the same reads? (same reads, same reference)

[Francesco Lescai]

Thank you for the quick answer. I understand this.
But I run the analysis in MAQ and most of the reads are correctly mapped.
So why BWA doesn't map the same reads? (same reads, same reference)