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#56 SAM tag X0: Number of multihits per read
Hello,
Would it be possible to add to the sam output of bowtie an additional tag which reports the number of alignments which each read has?
BWA has such a tag called X0 which according to the manual is the "number of best hits". For example X0:i:1 means the read has one reported alignment, X0:i:10 ten reported alignments etc. For downstream analysis, this would make easier to select reads according to their multimapping characteristics.
Many thanks!
Dario