From Cenny.Taslim at nationwidechildrens.org Wed Feb 2 10:05:31 2022 From: Cenny.Taslim at nationwidechildrens.org (Taslim, Cenny) Date: Wed, 2 Feb 2022 17:05:31 +0000 Subject: [maker-devel] Repbase subscription Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Feb 2 10:17:52 2022 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 2 Feb 2022 10:17:52 -0700 Subject: [maker-devel] Repbase subscription In-Reply-To: References: Message-ID: 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 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 > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1376 bytes Desc: not available URL: From Cenny.Taslim at nationwidechildrens.org Wed Feb 2 10:05:31 2022 From: Cenny.Taslim at nationwidechildrens.org (Taslim, Cenny) Date: Wed, 2 Feb 2022 17:05:31 +0000 Subject: [maker-devel] Repbase subscription Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Feb 2 10:17:52 2022 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 2 Feb 2022 10:17:52 -0700 Subject: [maker-devel] Repbase subscription In-Reply-To: References: Message-ID: 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 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 > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1376 bytes Desc: not available URL: From Cenny.Taslim at nationwidechildrens.org Wed Feb 2 10:05:31 2022 From: Cenny.Taslim at nationwidechildrens.org (Taslim, Cenny) Date: Wed, 2 Feb 2022 17:05:31 +0000 Subject: [maker-devel] Repbase subscription Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Feb 2 10:17:52 2022 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 2 Feb 2022 10:17:52 -0700 Subject: [maker-devel] Repbase subscription In-Reply-To: References: Message-ID: 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 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 > _______________________________________________ > maker-devel mailing list > maker-devel at yandell-lab.org > http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1376 bytes Desc: not available URL: