count.clips | R Documentation |
Takes GRanges or GappedAlignments object and uses cigar field (or takes character vector of cigar strings) and returns data.frame with fields (for character input) $right.clips number of "right" soft clips (e.g. cigar 89M12S) $left.clips number of "left" soft clips (e.g. cigar 12S89M), or appends these fields to the reads object
count.clips(reads)
reads |
GenomicRanges or GappedAlignments or data.frame or data.table holding the reads |
GRanges with 'right.clips' and 'left.clips' columns added
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