how to extract intron coordinates (in bed) from bam
I have aligned raw RNA-seq reads against a reference genome with STAR. I would like to extract the intronic coordinates from obtained bam files. Any suggestion?
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Devon Ryan
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praasu •
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praasu •
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This isn't information that one extracts, since it's not held within the BAM files. Instead your steps will be:
- Determine where transcripts and exons are (e.g. with stringTie).
- Process the resulting GTF file to retrieve introns (using whatever definition of this you'd like).
The second step may require some custom code, depending on whether you want introns that overlap exons (e.g., due to having multiple transcripts for a gene) or not.
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Devon Ryan
Did you use a strand-specific library prep?
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Then you can't know which strand the transcripts are from.
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Devon Ryan
You need to tell your aligner and stringTie that.
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