How to identify TSS sites from bacterial RNA-Seq data?
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.
• 4,886 views
•
link
updated
by
Charles Plessy
•
written
by
R.Blues
•
written
by
R.Blues
2 answers
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.
• 0 views
•
link
written
by
Charles Plessy
I used TSSer As input you need RNA-Seq from whole transcripts and 5-prime enriched
• 0 views
•
link
written
by
anne.de.jong •
Log in to answer this question.
More posts like this
-
Finding mutations by Ilumina rna-seq data
written by Deepblue •
-
Can I enrich a gene expression signature derived from single cell RNA-Seq in a bulk RNA-Seq data se…
written by miherbert •
-
Infer RNA-Seq library preparation from BAM
written by ResearchR
-
Detecting bacterial TSS from RNA-Seq data, how?
written by R.Blues
-
What is the correct way of using GTEx, CCLE and HPA data?
written by guto03 •
-
Operon prediction in RNA-Seq - How?
written by R.Blues
-
Getting RNA sequence from RNA-Seq reads; some questions
written by R.Blues
-
Is it possible to integrate RNA-seq data with ChIP-seq data if don't have "differential expression"…
written by nash.claire
-
Polyadenylation cleavage sites detection from rRNA-depleted RNA-Seq
written by Nicolas Rosewick
-
Copy Number Variation from paired end RNA-Seq data
written by ChIP
Have you tried DESeq from bioconductor?
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.
Here you have some examples http://web1.sph.emory.edu/users/hwu30/teaching/bioc/sgseq-lab.R