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wassermanlab / BiasAway

GNU Lesser General Public License v3.0
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hg38 background #4

Closed easwaranramamurthy closed 4 years ago

easwaranramamurthy commented 4 years ago

Is there a link from which I can download 1000bp background sequences for hg38? Thanks!

oriolfornes commented 4 years ago

Hi, @amathelier is reprocessing the background sequences for hg38. Please follow his reply here.

amathelier commented 4 years ago

Hi,

We're working on an update of BiasAway and will provide many background sequences soon. Let me get back to you next week.

Best AM

-- sent from my Samsung S7

On Thu, Jun 25, 2020, 20:58 Oriol Fornes notifications@github.com wrote:

Hi,

Thank you for your interest in BiasAway. Unfortunately, we do not provide background sequences for hg38. You can either generate them using the provided instructions in the README https://github.com/wassermanlab/BiasAway/blob/master/README file or liftOver the hg19 background sequences http://cisreg.cmmt.ubc.ca/BiasAway_background/human_BiasAway_bg/background_GCbins_crgmappable36mer_trim1000bp_all.tar.bz2 to hg38.

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easwaranramamurthy commented 4 years ago

Thanks!

amathelier commented 4 years ago

Dear Easwaran,

You can find newly generated background on Zenodo at https://doi.org/10.5281/zenodo.3923866. Note that we are working on an improved BiasAway. We are almost done with the new version, which is available at https://bitbucket.org/CBGR/biasaway/ https://bitbucket.org/CBGR/biasaway/src/master/ with a dedicated web-app currently hosted at http://testbiasaway.uio.no that will become available at http://biasaway.uio.no soon.

Best AM

On 25/06/2020 22:36, Easwaran Ramamurthy wrote:

Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/wassermanlab/BiasAway/issues/4#issuecomment-649804488, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA6Q4UEOU4OWGMVGGVQHJW3RYOYODANCNFSM4OIRSDFA.

-- Anthony

easwaranramamurthy commented 4 years ago

Thanks! This is really useful 👍