[miso-users] Required SAM format

[Alexander Kanitz]

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)?
And most importantly: in what format (one line, separate lines, CIGAR
string, MD tag, etc) do split/spliced alignments have to be represented?

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).

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
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