I'm trying to find all the reads (by name) from a BAM file that align to various regions in a bed file. Right now I can do this with bedtools using intersectBed:
intersectBed -abam reads.bam -wo -f 1 -b regions.bed -bedFrom this one can parse all the read ids that land in every interval in regions.bed, but it's not very compact. Is there a way to get bedtools to natively transform this into a more compact format, e.g.
chr1 x y .... read_id1,read_id2,read_id3where chr1 x y is a given interval in regions.bed and the comma separated read_id1,... is the list of read ids from reads.bam that fall in that interval. In this compact format, the output BED file would have at most as many entries as there are regions in regions.bed, whereas with the -wo option it can be even larger than the number of reads in reads.bam. Thanks.