BAM-to-Junction-BED
Uses SAMTools, Python 2.7 and PySam to extract either junctions or exon read counts for known and novel junctions and exons. Requires an indexed BAM file with genomic coordinates.
Example Commands
Produce a junction.bed coordinate file from a BAM file
python BAMtoJunctionBED.py --i /Users/me/sample1.bam
Produce a junction.bed coordinate file from a BAM file without strand predictions (e.g., STAR)
python BAMtoJunctionBED.py --i /Users/me/sample1.bam --g /Application/BAM-to-Junction-BED/ReferenceExonCoordinates/Mm_Ensembl_exon_Mm10.txt
Batch analysis of many BAM files in a single directory to obtain junction.bed and exon.bed results
python multiBAMtoBED.py --i /Users/me/BAMfiles --g /Application/BAM-to-Junction-BED/ReferenceExonCoordinates/Hs_Ensembl_exon_hg19.txt --r /Users/me/ExonBEDRef/Hs_Ensembl_exon-cancer_hg19.bed --a exon --a junction --a reference
Produce a junction.bed coordinate file from a BAM file using multi-processing
python multiBAMtoBED.py --i /Users/me/BAMfiles --a junction --m yes
Produce an exon.bed file using a reference bed file created by multiBAMtoBED or custom coordinates
python BAMtoExonBED.py --i /Users/me/sample1.bam --r /Users/me/Hs_exon-cancer_hg19.bed"