Reference Code backup Executable files
For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED format, this program will compare detected splice junctions to reference gene model. splicing annotation is performed in two levels: splice event level and splice junction level.
junction_annotation.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. | |
| -r REF_GENE_MODEL, --refgene=REF_GENE_MODEL | |
| Reference gene model in bed format. This file is better to be a pooled gene model as it will be used to annotate splicing junctions [required] | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). [required] | |
| -m MIN_INTRON, --min-intron=MIN_INTRON | |
| Minimum intron length (bp). default=50 [optional] | |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be considered as “uniquely mapped”. default=30 | |