Reference Code backup Executable files
Calculate the distributions of clipped nucleotides across reads
clipping_profile.py -i Pairend_StrandSpecific_51mer_Human_hg19.bam -s "PE" -o out
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_FILE, --input-file=INPUT_FILE | |
| Alignment file in BAM or SAM format. | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be considered as “uniquely mapped”. default=30 | |
| -s LAYOUT, --sequencing=LAYOUT | |
| Sequencing layout. “SE”(single-end) or “PE”(pair-end). | |