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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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Is there a hg38 version VastDB ? #58

Closed ZheFrench closed 7 years ago

ZheFrench commented 7 years ago

Hi,

It's more a question than an issue.

Do you plan to create/share a new VastDB specifically for hg38 ?

I saw that you lift over results from the hg19 to hg38. So I was wondering...

Thanks

mirimia commented 7 years ago

Hi,

It may eventually be done, but it's currently not a major priority (as the liftover does the job quite well!).

Cheers Manu

ZheFrench commented 7 years ago

Yeah but you are loosing last annotated exons in hg38 that can be spliced. Even if you lift over to hg38. The ones not present in hg19 still remains unfound.

2017-02-27 17:15 GMT+01:00 Manuel Irimia notifications@github.com:

Hi,

It may eventually be done, but it's currently not a major priority (as the liftover does the job quite well!).

Cheers Manu

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vastgroup/vast-tools/issues/58#issuecomment-282766924, or mute the thread https://github.com/notifications/unsubscribe-auth/ANWiGOZi0truVdj-Ob5u7Phlywe4_Zlsks5rgvaxgaJpZM4MJqYZ .

-- Jean-Philippe Villemin - Bioinformatics, Software Engineer -

IGH (Institute of Human Genetics)

Team: Splicing and Epigenetics 141 rue de la Cardonille Montpellier France 4094 cedex 5

jpvillemin@gmail.com jpvillemin@gmail.com

mirimia commented 7 years ago

But that seems more an issue of annotation than assembly, for what you say...

ZheFrench commented 7 years ago

Yeah totally but do vastdb is not also related to annotation ? I do not know what it contains. Sorry :)

2017-02-27 17:21 GMT+01:00 Manuel Irimia notifications@github.com:

But that seems more an issue of annotation than assembly, for what you say...

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/vastgroup/vast-tools/issues/58#issuecomment-282768976, or mute the thread https://github.com/notifications/unsubscribe-auth/ANWiGBG68_7g_OaycvEv66XZO9TstPLcks5rgvghgaJpZM4MJqYZ .

-- Jean-Philippe Villemin - Bioinformatics, Software Engineer -

IGH (Institute of Human Genetics)

Team: Splicing and Epigenetics 141 rue de la Cardonille Montpellier France 4094 cedex 5

jpvillemin@gmail.com jpvillemin@gmail.com

mirimia commented 7 years ago

Yes, it is an annotation set. What I meant is that it could also be improved/enriched using hg19.