How to identify TSS sites from bacterial RNA-Seq data?
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5.1 years ago
R.Blues ▴ 150

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 • 2.8k views
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Have you tried DESeq from bioconductor?

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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.

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5.0 years ago
Charles Plessy ★ 2.8k

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

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

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5.0 years ago
anne.de.jong ▴ 10

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

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

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