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vpc-ccg / circminer

A sensitive and fast tool for circular RNA detection from RNA-Seq data
GNU General Public License v3.0
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CIGAR string #5

Open fhach opened 4 years ago

fhach commented 4 years ago

Any plans on adding CIGAR strings to SAM output so I can load the alignments in a genome browser?

Originally posted by @yhoogstrate in https://github.com/vpc-ccg/circminer/issues/4#issuecomment-649549131

yhoogstrate commented 4 years ago

Since the CIGAR's N blocks do not support negative numbers (for back splicing), it is in practice impossible to use one SAM segment to describe the alignment of a back spliced read entirely.

I believe that it is common practice to split a backspliced read in two and use two aligned segments of which the counter-part is soft-clipped. Of those two segments, one (typically last part of the read) is set to 'supplementary/secondary alignment'. Both split alignments/segments then should have an 'SA' tag in place to reference each other. (http://samtools.github.io/hts-specs/SAMtags.pdf ; page 4)