I have very basic question about bam files, it may be very obvious but kind of stacked.
I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats of LINE/SINE etc. elements).
For this, I have aligned data in bam format and the repeats in bed format.
As far as i know BAM files contains aligned data for each read from fastq file. How can i summarise information for each gene from a bam file? so that i can overlap these genes with the repeats and check for an enrichment?
I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats of LINE/SINE etc. elements).
For this, I have aligned data in bam format and the repeats in bed format.
As far as i know BAM files contains aligned data for each read from fastq file. How can i summarise information for each gene from a bam file? so that i can overlap these genes with the repeats and check for an enrichment?
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