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Notes on SAM/BAM files created by BSmooth #19

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PeteHaitch opened this issue Aug 19, 2013 · 2 comments
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Notes on SAM/BAM files created by BSmooth #19

PeteHaitch opened this issue Aug 19, 2013 · 2 comments
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@PeteHaitch
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SAM/BAM files created by BSmooth contain the read sequence in the YO tag rather than in the SEQ field. In fact, the SEQ field contains the C-to-T converted sequence.

More generally, it appears the SAM/BAM files created by bsmooth may not comply with SAM specifications.
@PeteHaitch
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When using the --fr flag to indicate that reads should be in FR orientation (the default for Illumina's paired-end sequencing protocol) the FLAG is set to either 67 or 131. This is not what I expect. I would expect 99 or 147. Need to check my reasoning by eyeballing some reads in IGV.

@ghost ghost assigned PeteHaitch Jan 14, 2014
@PeteHaitch PeteHaitch mentioned this issue Jan 14, 2014
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@PeteHaitch PeteHaitch mentioned this issue Aug 15, 2014
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@PeteHaitch
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Closing for now. See #87 for general discussion on support for additional aligners.

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