How to identify Transcription start sites (TSS)

Question

[vimlakany]

How to identify Transcriptional Start Site (TSS) from Mycobacterium RNA-Seq data?

[GouthamAtla]

You can not identify the TSS from RNA-Seq. You need CAGE-Seq or GRO-Seq for that.

Answer 1

[Whoknows]

You could use Homer software for finding TSS regions.

I have copied below command from Homer , read Custom Annotations section precisely: First, you need to convert your bam/sam to bed (bedops works nice) and download GTF file from UCSC website, then run this command:

annotatePeaks.pl ERpeaks.bed hg18 -gtf gencode.gtf  > outputfile.txt

[Daniel]

Could you describe how you do this? I can't see a methodology for it in their documentation.

[Whoknows]

please see the update.