[miso-users] Required SAM format

[Alexander Kanitz]

Dear Yarden,

thanks a lot for the info.

I have since looked at some recent TopHat outputs.

Since we are following quite a complicated (read: "sophisticated" ;)
mapping strategy (map against gen and trx, map the trx coordinates back to
gen, merge files, keep best alignments and discard non-unique primary
alignments), re-creating the SAM file was anyway required, and the
conversion to the required output should be easy.

Thanks a lot for your help and enjoy your travels!

Best,
Alex



On Fri, Aug 16, 2013 at 8:29 PM, Yarden Katz <yarden at mit.edu> wrote:

> Hi Alex,
>
> See comments below:
>
> On Aug 13, 2013, at 6:56 AM, Alexander Kanitz wrote:
>
> > Hi everyone,
> >
> > I am planning to use MISO but I want to be flexible with the aligner I
> use (read: don't want to use Bowtie/TopHat).
> >
> > Since I did not find any detailed specs regarding this issue, I have a
> few questions:
> > What does MISO need out of a SAM/BAM file? Specifically, which tags are
> considered and which are required (assuming all others will be ignored)?
>
> MISO tries to not rely on too many binary SAM/BAM flags since as you imply
> many different aligners follow slightly different conventions.
>
> The main flags used as strandedness if you have stranded data and
> paired-ness/orientation of reads if you have paired-end data.  There's a
> flag to MISO that can tell it to group read pairs by ID, e.g. assuming that
> the reads have the format:
>
> readX/1
> readX/2
>
> or something similar that makes it clear that they are both mates of the
> same sequenced molecule.
>
> > And most importantly: in what format (one line, separate lines, CIGAR
> string, MD tag, etc) do split/spliced alignments have to be represented?
>
> CIGAR string.  I can add a note to the manual clarifying this.
>
>
> >
> > I would be very grateful for some help here and ideally a few lines of a
> MISO-compatible SAM file including some split/spliced alignments if
> possible (or a link to such a file).
>
> Any BAM file produced with Tophat and Bowtie 1 should be an example of a
> MISO-accepted BAM, and we normally use Tophat around here though have users
> that use other aligners.  I am traveling and don't have access handy now,
> but it should be easy to find.
>
> One thing to note: MISO ignores insertions and deletions as they do not
> match the annotation -- so any reads with insertion/deletions in their
> CIGAR strings will be discarded.
>
> >
> > Thanks a lot!
> >
> > Best,
> > Alex
> >
> >
> > --
> > Alexander Kanitz, Ph.D.
> >
> > Winterthurerstrasse 358
> > 8057 Zurich
> > Switzerland
> >
> > Phone: +41 76 278 39 36
> > Email: alexander.kanitz at alumni.ethz.ch
> > _______________________________________________
> > miso-users mailing list
> > miso-users at mit.edu
> > http://mailman.mit.edu/mailman/listinfo/miso-users
>
>


-- 
Alexander Kanitz, Ph.D.

Winterthurerstrasse 358
8057 Zurich
Switzerland

Phone: +41 76 278 39 36
Email: alexander.kanitz at alumni.ethz.ch
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