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Ribo-SeqR input preparation - rosario.avolio - 04-Oct-2017 04:04 PM

Hi everyone,

first of all thank you for the RiboGalaxy tools, I am trying to analyze my RP data but I am a beginner in bioinformatic analysis so I found it very useful!

I have a (probably silly) question for you. I have 2 conditions 3 replicates each. When I prepare the riboSeqR input using the appropriate tool which is the best way to proceed? Choosing one "Ribo seq alignment" and the 3 corresponding replicates SAM file together or it is better to run one SAM file (so 1 replicate) at time?

Thank you in advance for the reply


RE: Ribo-SeqR input preparation - audrey - 04-Oct-2017 04:21 PM

Hi Rosario,

It is a good question.

I think it would be best to initially run the riboSeqR tool on each SAM file separately so that you can get a sense if the triplet periodicity/metagene analysis is similar across the individual samples. This would also help determine if there are any issues.

If your intention is to then use the differential translation analysis component of riboSeqR (baySeq), then you would need to re-do the Prepare riboSeqR input, Triplet Periodicity and Metagene Analysis steps. In the Prepare riboSeqR input step, include the 3 corresponding replicate SAM files for each replicate group.

If you encounter any issues let us know.

All the best,