Reference Code backup Executable files
Calculate the RNA-seq reads coverage over gene body.
geneBody_coverage.py -r hg19.housekeeping.bed -i test.bam -o output
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_FILES, --input=INPUT_FILES | |
| Input file(s) in BAM format. “-i” takes these input: 1) a single BAM file. 2) ”,” separated BAM files. 3) directory containing one or more bam files. 4) plain text file containing the path of one or more bam file (Each row is a BAM file path). All BAM files should be sorted and indexed using samtools. | |
| -r REF_GENE_MODEL, --refgene=REF_GENE_MODEL | |
| Reference gene model in bed format. [required] | |
| -l MIN_MRNA_LENGTH, --minimum_length=MIN_MRNA_LENGTH | |
| Minimum mRNA length (bp). mRNA smaller than “min_mRNA_length” will be skipped. default=100 | |
| -f OUTPUT_FORMAT, --format=OUTPUT_FORMAT | |
| Output file format, ‘pdf’, ‘png’ or ‘jpeg’. default=pdf | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). [required] | |