Suggestions for improvements

[kvittingseerup]

I think GREIN is a really usefull tool but have two suggestions for imporvements:

• Make abundances downloadable as well - many people would be interested in that and the improved abundance estimates are one of the main features of a Salmon quantification.
• If you re-run the pipeline I would wish for running salmon with the bias correction (--seqBias and --gcBias) since those are some of the main features of Salmon.

[naimmahi]

Thanks for your comments and suggestions. We really appreciate it.

• By abundance estimates, do you mean the transcript level abundances provided by Salmon? We do provide that but in a rounded format.
• That's a great suggestion. Currently, we run Salmon with the default options but definitely we do have the flexibility to add other options too.

[kvittingseerup]

• Yes I meant the transcript level abundances (TPM) values.
• Based on the Salmon paper I do think especially the gcBias algorithm would be very usefull when you are quantifying such a diverse sets of data.

[naimmahi]

Providing TPM would be trivial and it will be available in the next release. Regarding gcBias, we are planning to add it in our pipeline for further data processing.

Thanks.

[kvittingseerup]

Hi @naimmahi

I have 3 small questions:

• Do you have an idea when the next release will be?
• Is it necessary to round (count and) abundances to integers? (could it be rounded to a couple of digits)
• Is there a way to download the datasets without going through the Shiny interface (if one wants to analyse more than a few datasets that becomes tiresome)?. Kinda like what you can do via the recount R package.

Cheers Kristoffer

[naimmahi]

Hi @kvittingseerup

• We have updated and added several new features in GREIN. You can now download both the raw and normalized (CPM and TPM) data in the original form. Although we show the raw gene level data in rounded format but the downloadable file is in it's original form.

• We do have this in our consideration. We already have a processing package GREP2 and we are thinking of adding this downloading feature as well within this package.

Thanks.

[kvittingseerup]

Hi @naimmahi

Any news on the option for batch downloading the re-quantified data?

Cheers Kristoffer

[naimmahi]

Hi @kvittingseerup Unfortunately this feature will not be available because providing analysis options at individual dataset level is the whole purpose of GREIN. We had thought about it and decided not to proceed with it. Sorry about that and thanks again.

[kvittingseerup]

Hi @naimmahi Thanks for letting me know - and I do understand :-) Thanks again for making GREIN available.

Cheers Kristoffer