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!
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!
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