How to identify Transcriptional Start Site (TSS) from Mycobacterium RNA-Seq data?
You can not identify the TSS from RNA-Seq. You need CAGE-Seq or GRO-Seq for that.
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
Could you describe how you do this? I can't see a methodology for it in their documentation.
please see the update.
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