Reference Code backup Executable files
Calculate fragment size for each gene/transcript. For each transcript, it will report : 1) Number of fragment that was used to estimate mean, median, std (see below). 2) mean of fragment size 3) median of fragment size 4) stdev of fragment size
RNA_fragment_size.py -r hg19.RefSeq.union.bed -i SRR873822_RIN10.bam > SRR873822_RIN10.fragSize
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_FILE, --input=INPUT_FILE | |
| Input BAM file | |
| -r REFGENE_BED, --refgene=REFGENE_BED | |
| Reference gene model in BED format. Must be strandard 12-column BED file. [required] | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be called “uniquely mapped”. default=30 | |
| -n FRAGMENT_NUM, --frag-num=FRAGMENT_NUM | |
| Minimum number of fragment. default=3 | |