Transcription start site mapping and counts

I modified the RNA-Seq protocol, so that 5’ end adapters were ligated prior to RNA fragmentation and 3’-end adapter ligation. I have mapped the reads to a reference bacterial genome. Now I would like to get a list of the 5’ start positions (transcription start sites) along with the frequency of occurrence for each starting position. What is the best way to do this?

Chaitanya Jain

Dear @cjain,
There is a tools at least on the, which is called “Extract alignment ends from SAM or BAM”. With that you get the 5’ and 3’ ends in bed format. To count your start or ends sites your can use “Count occurrences of each record”. If you are operating on or other instances without the first tool, then what you can do is to convert the bam into a bed file with “bedtools BAM to BED converter”.

I hope I could help.

Best wishes,

Thank you very much for your suggestions! That does seem to nicely solve my issues.