<div dir="ltr">Hi everyone,<div><br></div><div>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). </div><div><br></div><div>Since I did not find any detailed specs regarding this issue, I have a few questions:</div>
<div>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)? </div><div>And most importantly: in what format (one line, separate lines, CIGAR string, MD tag, etc) do split/spliced alignments have to be represented?</div>
<div><div><br></div><div>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).</div><div><br></div>
<div>Thanks a lot!</div><div><br></div><div>Best,</div><div>Alex</div><div><br></div><div><br></div>-- <br>Alexander Kanitz, Ph.D.<br><br>Winterthurerstrasse 358<br>8057 Zurich<br>Switzerland<br><br>Phone: +41 76 278 39 36<br>
Email: <a href="mailto:alexander.kanitz@alumni.ethz.ch" target="_blank">alexander.kanitz@alumni.ethz.ch</a><br>
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