[gwilymh]

If I understand your question correctly, BEDTools has a utility called coverageBed that will compute the raw counts of reads in a BAM file among features in a BED or GTF file.

For example:

$ coverageBed -abam alignedReads.bam -b transcripts.gtf > transcript.cov.txt

There is also a histogram (-hist) mode that will give you a histogram of coverage for each feature in the -b file. I have not yet updated the manual , but the help (-h) for this tools describes the output format.

Just to clarify, is the depth of coverage of each feature synonymous with the raw counts of reads?

[wanfahmi]

How can I get a read count per exon per transcript in a particular gene from BAM file? I tried using htseq-count with id_attr=transcipt_id but this approach does not give me the read count per exon per transcript. I tried using DEXSeq to get the read count, but it does not get what I want. Is there any way to get the read count? I only got one gene of interest to analyse which TPM1. This gene has more than 40 isoforms, so it is possible to get each of the isoforms their read count for each exon. Thanks!