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 bases and the counts of the reads.

4.1.1 Parameters

4.1.1.1 Input

--bam Input_bam_file.bam

Input BAM file

4.1.1.2 Specific

--writeReads readsFile.txt.gz	Will write alignments with softclipping to file.
--printSequences	Will write alignments with softclipping to file (combine with --writeReads).
--printAll	Write for all reads (combine with --writeReads).

4.1.1.3 Engine

• General
• Bases
• Reads
• Genome

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.

4.1.3 Usage Example

# Simulate a BAM File
atlas simulate

# Assess softclipped bases
atlas assessSoftClipping --bam ATLAS_simulations.bam