Hi all,

Recently I have tried to analyse direct RNA seq data, and I started looking at length of polyA tail length. Using nanopolish (using fast5 files and previously aligned bam files) I have lists of reads (reads name/ID) and their corresponding genomic location (chr and position) where the polyA tail starts, and the estimated tail length for each read. Now I'm would like to see which gene/transcript each individual read was actually mapped to, which unfortunately isn't provided in the analysis. I am trying to generate list of chr/position as bed file to bedtools and match it up with GTF file using bedtools closest (bedtools closest -t first -D a -id -s). However, it's struggling to distinguish genes/transcripts that are closed together. I'm just wondering whether there is a way to extract mapping information from bam file to generate a complete list of where every single read (read ID/name) and which transcript/gene the read is mapped to? If there's a way to do this then I can quickly match up polyA length for each gene/transcript.

Any help or comments would be much appreciated!

Josh