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Why is mappability removed? #7

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magicDGS opened this issue May 1, 2018 · 19 comments

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@magicDGS
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commented May 1, 2018

One of my main usages of gem-mapper is to compute a mappability track, but I just found that it is removed in the latest commit to master. Is there any plan to include it again in a follow-up commit? Otherwise, is there any other software to compute the same mappabiltiy track as gem?

Thank you!

@smarco

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commented May 1, 2018

@magicDGS

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commented May 2, 2018

Thanks for the quick answer, Santiago. I tried to find the old version of mappability at http://gemlibrary.sourceforge.net, but it redirects to http://dat.cnag.cat/wiki/The_GEM_library, which is returning a 404 response. Thus, I cannot access the old binaries anymore - do you have any clue why the page is not longer available?

@smarco

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commented May 2, 2018

@magicDGS

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commented May 3, 2018

Thanks!

@magicDGS

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commented Jul 3, 2018

Any news about the mappability tool?

@smarco

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commented Jul 9, 2018

It's our intention to release soon a fully functional version within the next update of the tool.

For the time being, you can use the old mappability tool at https://sourceforge.net/projects/gemlibrary/files/gem-library/

Sorry for the inconvenience,

@lldelisle

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commented Oct 2, 2018

Hi,
I would need the gem-mappability in galaxy. If you are close to update I would prefer to wait and use the last version. Could you tell me if you have an idea of the date?
Thank you very much,

Lucille

@smarco

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commented Oct 2, 2018

Hi Lucille,

Thought I'm actively working on it, I cannot guarantee that the new mappability will be released before a couple of months. I'm really sorry about any inconvenience it can cause.

Please, use the current mappability tool for the moment (https://sourceforge.net/projects/gemlibrary/files/gem-library/).

Thanks for using GEM,

@lldelisle

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commented Oct 2, 2018

Many thanks for the reply.

@splaisan

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commented Nov 30, 2018

Also an old and enthusiast user of mappability and adding my vote here to get the new version as soon as you can make it.
Thanks in advance
Stephane

@duartemolha

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commented Jul 15, 2019

Hi ... I followed the description here
https://wiki.bits.vib.be/index.php/Create_a_mappability_track

but I had created the index using the latest version of gem-indexer

gem-mappability complains about the header of the index file

is the index file for the latest version of gem3-mapper incompatible with the archive version?

Thanks

@splaisan

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commented Jul 15, 2019

Hi @duartemolha,
please read [https://github.com//issues/10](this other note) to solve the issue

@duartemolha

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commented Jul 15, 2019

Hi @duartemolha,
please read [https://github.com//issues/10](this other note) to solve the issue

Thanks but I believe the problem I encountered is before the gem-2-wig step... I am failing to produce the mappability file ...

create mappability track

This step :

gem-mappability -T 8 -I hg38_index.gem -l 150 -o hg38_index_150

@smarco

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commented Jul 15, 2019

Hi @duartemolha,

Please make sure you are generating the index using the same version as the mappability (https://sourceforge.net/projects/gemlibrary/files/gem-library/). Note that GEM3 indexes are not backwards compatible.

@duartemolha

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commented Jul 16, 2019

thanks

I understand now

@duartemolha

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commented Jul 16, 2019

any update on when mappability might be incorporated back into the software?

@VidJa

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commented Jul 16, 2019

May I vote for the mappability option as well?

@duartemolha

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commented Jul 16, 2019

BTW... I am creating a mappability at 150bp for the latest human reference hg38. Do you know if someone has already done that? I am running it in a pretty powerful server and I estimate it will take at least 24 hours

@smarco

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commented Jul 16, 2019

Honestly, I cannot commit to any specific deadline, but I can assure you it's among my top priorities.

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