Question: How to identify TSS sites from bacterial RNA-Seq data?
2
gravatar for R.Blues
3 months ago by
R.Blues50
Somewhere
R.Blues50 wrote:

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.

tss rna-seq • 237 views
ADD COMMENTlink modified 10 weeks ago by Charles Plessy1.5k • written 3 months ago by R.Blues50

Have you tried DESeq from bioconductor?

ADD REPLYlink written 10 weeks ago by Lila M 210

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.

ADD REPLYlink written 10 weeks ago by R.Blues50

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

ADD REPLYlink written 10 weeks ago by Lila M 210
1
gravatar for Charles Plessy
10 weeks ago by
Charles Plessy1.5k
Japan
Charles Plessy1.5k wrote:

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.

image from the website

ADD COMMENTlink written 10 weeks ago by Charles Plessy1.5k

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

ADD REPLYlink written 10 weeks ago by R.Blues50
0
gravatar for anne.de.jong
10 weeks ago by
anne.de.jong0 wrote:

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

ADD COMMENTlink written 10 weeks ago by anne.de.jong0

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

ADD REPLYlink written 10 weeks ago by R.Blues50
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