Reference Code backup Executable files
Calculate inner distance between read pairs.
inner_distance.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12
| --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) | |
| -r REF_GENE, --refgene=REF_GENE | |
| Reference gene model in BED format. | |
| -k SAMPLESIZE, --sample-size=SAMPLESIZE | |
| Number of read-pairs used to estimate inner distance. default=1000000 | |
| -l LOWER_BOUND_SIZE, --lower-bound=LOWER_BOUND_SIZE | |
| Lower bound of inner distance (bp). This option is used for ploting histograme. default=-250 | |
| -u UPPER_BOUND_SIZE, --upper-bound=UPPER_BOUND_SIZE | |
| Upper bound of inner distance (bp). This option is used for plotting histogram. default=250 | |
| -s STEP_SIZE, --step=STEP_SIZE | |
| Step size (bp) of histograme. This option is used for plotting histogram. default=5 | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be called “uniquely mapped”. default=30 | |