Extract reads mapping to unannotated regions

Question

[kachroo.priyanka]

Hi,

I have single-end 75bp reads from RNASeq data mapped to bacterial reference genome via EDGE-pro software. I observed that only around 70% of mapped reads appear to be falling within annotated genes (start and stop coordinates provided to the aligner via .ptt and .rnt files). From the bam file, is there a way to extract reads mapping to the reference but falling outside the annotated regions. I would like to know where in the genome are these reads mapping to e.g. gene boundary/ UTR etc.

Thanks, Priyanka

Answer 1

[Devon Ryan]

bedtools intersect -v -wa -a alignments.bam -b genes.gtf > non_genic.bam