Hello! I need to filter peaks which are withwin gene regions. I have .bam file from CHIP-seq experiment and .bam file from RNA-seq. I am trying to do this with this command:
bedtools intersect -a A.bam -b B.bam > AB.bam
The problem is that the output AB.bam is exactly the same as A.bam (it is visuable in IGV). Can someone give some advices?
1 answer
I don't know what is going wrong with the command you are using. But to filter peaks in that are in gene regions, I would normally do
bedtools intersect -u -a peaks.bed -b geneset.gtf
Where peaks.bed is the output of a peak caller (and if it was MACS then the file would be .narrowPeak or .broadPeak not .bed) and geneset.gtf is either annotation downloaded from an annotation database (e.g. refseq or ENSEMBL) or is created from the RNAseq using a transcript assembly program like stringtie. The -u means Write original A entry once if any overlaps found in B.
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Can you add a few lines of A.bam and B.bam? especially lines that show some of the intersections? You can modify the data if it's confidential, but if you add more details you'll get better answers. Also, check out similar questions that appears on the right section of your post.
Try adding one of these options:
https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html