[maker-devel] Repbase subscription

[Taslim, Cenny]

This is good to know. Unfortunately our university library does not have a Repbase license.

From: Fields, Christopher J <cjfields at illinois.edu>
Sent: Tuesday, March 22, 2022 11:12 AM
To: Taslim, Cenny <Cenny.Taslim at nationwidechildrens.org>; Carson Holt <carsonhh at gmail.com>
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Repbase subscription

A small note on this: if you have an academic affiliation, a number of academic institutions have Repbase licenses through their libraries (much like a journal). For example, this one from the U. of Illinois, which requires login to access.

A small note on this: if you have an academic affiliation, a number of academic institutions have Repbase licenses through their libraries (much like a journal).  For example, this one<https://urldefense.com/v3/__https:/i-share-uiu.primo.exlibrisgroup.com/discovery/fulldisplay?docid=alma99908209112205899&context=L&vid=01CARLI_UIU:CARLI_UIU&search_scope=MyInstitution&tab=LibraryCatalog&lang=en__;!!NiUAmZJ8c1GNWg!UVhpFdTL43YRyH5cVMr6ZmLDDcspa33Cvu0EemZKJoMJZFv89jxzaFC38oktIIt7Y4aji_AWC7E3m1c0EeAx5eDuIMJPD9JSdQ$> from the U. of Illinois, which requires login to access.

chris
On Feb 2, 2022, 11:18 AM -0600, Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, wrote:

Yes. Do a manual install of RepeatMasker with HMMER as the aligner and Dfam as the reepeat database (free). Run RepeatModeler to get an assembly specific repeat dataset and give that to MAKER. The combination of the two will allow you to mask sufficiently for the annotation.  If for any reason you want to classify the repeats into families for further analysis rather than just mask them out, then you want a RepBase subscription.

—Carson



On Feb 2, 2022, at 10:05 AM, Taslim, Cenny <Cenny.Taslim at nationwidechildrens.org<mailto:Cenny.Taslim at nationwidechildrens.org>> wrote:

Hi,

I just have a quick question before spending time to install maker. Now that Repbase requires active subscription as of April 2019, it is possible to run maker without Repbase?

Thanks,
Cenny
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