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clipping_profile.py

Estimate the soft-clipping profile of RNA-seq reads. CIGAR strings must contain 'S' operations (the aligner must support clipped mapping).

Usage

clipping_profile.py -i input.bam -o output_prefix -s SE

Options

Option Description Default
-i, --input-file Alignment file in BAM or SAM format Required
-o, --out-prefix Prefix of output files Required
-s, --sequencing Sequencing layout: SE (single-end) or PE (paired-end) Required
-q, --mapq Minimum mapping quality for "uniquely mapped" 30

Output

  • prefix.clipping_profile.xls — clipping percentages per read position
  • prefix.clipping_profile.r — R script for clipping profile plot
  • prefix.clipping_profile.pdf — clipping profile plot (if R is available)