4.1 assessSoftClipping

Assessing level of soft clipping in BAM file

assessSoftClipping provides soft clipping statistics for all reads, i.e. the number of soft-clipped positions (??, their bases) and the counts of the reads.

4.1.1 Input

Required inputs :

--bam Input_bam_file.bam Input BAM file.

Optional inputs :

  • None

Specific Parameters :

  • None

Engine parameters that are common to all tasks can be found here.

4.1.2 Output

*_softClippingMatrixBoth.txt Text file with information about distribution of soft clipping on left and right sides of the read combined.
*_softClippingMatrixLeft.txt Text file with information about distribution of soft clipping on the left side of the read.
*_softClippingMatrixRight.txt Text file with information about distribution of soft clipping on the right side of the read.
*_filterSummary.txt A text file with filter summary.

4.1.3 Usage Example

#! /bin/bash

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --fixedSeed 30

out="assessSoftClipping"
$atlas --task assessSoftClipping --bam simulate.bam \
       --fixedSeed 31 --out $out --logFile $out.out 2> $out.eout