This tool provides soft clipping statistics for all reads, i.e. the number of soft-clipped positions and their bases.
a txt file with suffix _clippingStats.txt.gz with the following information:
- read name
- mapping position of read
- number of softclipped bases on the left side of the read
- number of bases that were not softclipped per read
- number of softclipped bases on the right side of the read
if the option printSequences is used, the sequences underlying these statistics are also written to file.
./atlas task=assessSoftClipping bam=example.bam printSequences
- printAll: Write softclipping stats for all alignments to file, also those that do not have any softclipping
- printSequences: Write softclipped sequences to file
Engine parameters that are common to all tasks can be found here.