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tleonardi / nanocompore

RNA modifications detection from Nanopore dRNA-Seq data
https://nanocompore.rna.rocks
GNU General Public License v3.0
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Raw data availability #115

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @tleonardi ,

Is your raw data from nanocompore paper available?. in the paper you said is available in ENA with accession PRJEB35148. But I could not find the raw data?

Also, I wanted to know that if your software can be used to detect any types of modifications, as long as there are two samples to do the statistical comparison?

Best, Vahid.

tleonardi commented 4 years ago

Hi @vahidAK, we are very happy to openly share the data. We had a couple of issues with the data upload to ENA, but these should be solved pretty quickly. Sorry about this. In the meantime, if you urgently need some specific datasets I'd be happy to send them to you in some other way.

Regarding your second question, yes: Nanocompore can in principle detect any RNA modification as long as: 1) the modification causes a measurable change in the electric signal and 2) you have a control condition that lacks the modification (or is strongly depleted).

Best, Tom

vahidAK commented 4 years ago

Great! thanks a lot @tleonardi , Please let me know when the data was available.

Best, Vahid.

tleonardi commented 4 years ago

Hi @vahidAK, the data is now available on ENA. You can find it under the accession number PRJEB35148. cheers! tom

lpryszcz commented 4 years ago

Hi @tleonardi , is the data still available at ENA? I've check today and PRJEB35148 lists only FastQ and .cram files. Cheers, Leszek

tleonardi commented 3 years ago

Hi @lpryszcz, yes, the fast5 files were converted to cram before uploading them to ENA, as we were told that cram has better compression. The conversion (both ways) can be done with this tool: https://github.com/EGA-archive/ont2cram

best tom