Hi,
I am trying to extract reads from a BAM file that cover 100% of a short feature (ie. small RNA species), but extend at either their 3' or 5' ends. I tried bedtools multicov with -f 1 and -r, but that only gives me reads that exactly span the feature, and excludes those that extend.
Is there a way to extract those reads?
I am trying to extract reads from a BAM file that cover 100% of a short feature (ie. small RNA species), but extend at either their 3' or 5' ends. I tried bedtools multicov with -f 1 and -r, but that only gives me reads that exactly span the feature, and excludes those that extend.
Is there a way to extract those reads?