How to identify TSS sites from bacterial RNA-Seq data?

Question

[R.Blues]

Hello all,

I know this has been asked a lot, but I am trying to predict TSS sites with bacterial RNA-Seq data (I have a reference genome and annotation). It is standard paired-end RNA-Seq data, not enriched or dRNA-Seq.

I know it can be done, but... I cannot find how. Which programme, R package, etc. can I use??

Thanks a lot.

[Lila M]

Have you tried DESeq from bioconductor?

[R.Blues]

No, I haven't! I didn't know it can be used for TSS discovery. Would you mind telling me how? I do not find any TSS mention in the manual.

[Lila M]

Here you have some examples http://web1.sph.emory.edu/users/hwu30/teaching/bioc/sgseq-lab.R

Answer 1

[Charles Plessy]

Perhaps you can try Parsec? It searchs for boundaries in RNA-seq data and therefore identifies transcription start and stop sites. The image below is linked from the Parsec website.

[R.Blues]

I'll give it a try and let you know. Thank you very much!!

Answer 2

[anne.de.jong]

I used TSSer As input you need RNA-Seq from whole transcripts and 5-prime enriched

[R.Blues]

Yes, I know, but I do not have 5-prime enriched data.