Question: How to identify TSS sites from bacterial RNA-Seq data?
2
gravatar for R.Blues
6 months ago by
R.Blues60
Somewhere
R.Blues60 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 • 362 views
ADD COMMENTlink modified 5 months ago by Charles Plessy2.0k • written 6 months ago by R.Blues60

Have you tried DESeq from bioconductor?

ADD REPLYlink written 5 months ago by Lila M 280

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 5 months ago by R.Blues60

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

ADD REPLYlink written 5 months ago by Lila M 280
1
gravatar for Charles Plessy
5 months ago by
Charles Plessy2.0k
Japan
Charles Plessy2.0k 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 5 months ago by Charles Plessy2.0k

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

ADD REPLYlink written 5 months ago by R.Blues60
0
gravatar for anne.de.jong
5 months 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 5 months ago by anne.de.jong0

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

ADD REPLYlink written 5 months ago by R.Blues60
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