[mira_talk] Re: Paired end info - SAM/BAM output from MIRA?
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 30 Sep 2010 20:22:13 +0200
On Donnerstag 30 September 2010 Peter wrote:
> MIRA3 puts a lot of stuff into RT lines (read tags). These might
> be stored in the SAM/BAM read tags...
These read tags actually help understanding some decisions MIRA made.
Especially useful in finishing, though I am not aware of any finishing
software using SAM/BAM as input.
Oh, and when doing SNP analysis, MIRA also tags SNPs in reads, not only in the
consensus (consensus tags).
> There are lots of things that could be added, like using the MAF
> ST and/or MT lines to record the sequencing type via the RG
> (read group) and PL (platform) tags. Perhaps also the SN lines
> (strain information) could be done with a SAM read group?
Would certainly be helpful.
> Perhaps I should look at MIRA's AO lines (as well as the AT
> line) when constructing a CIGAR string?
Hmmm ... I think you even have to if you want to reconstruct deletions in
reads.
> Note this is a Python script, and currently uses Biopython. That
> dependency could be avoided with a little more effort if there
> was demand for this (e.g. to include it with MIRA).
Depending on "little more effort" I would suggest delaying that until things
stabilise for the script. At the moment I suppose that Biopython helps you
developing more effectively, that should be your primary concern at the moment
:-)
B.
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