From ABoyher at danforthcenter.org Fri Nov 15 14:26:13 2019 From: ABoyher at danforthcenter.org (Boyher, Adam) Date: Fri, 15 Nov 2019 21:26:13 +0000 Subject: [maker-devel] Apply old maker gff to new assembly Message-ID: Hi I'm a bit unsure of how to apply a previous maker annotation to a new assembly. I just want a quick annotation, so just taking the genes that are already in the annotation file with their functional annotations and naming schemes and find those genes in the new assembly. Which settings should i use in maker_opts.ctl? Thanks Adam From scott at scottcain.net Mon Nov 18 20:28:32 2019 From: scott at scottcain.net (Scott Cain) Date: Mon, 18 Nov 2019 19:28:32 -0800 Subject: [maker-devel] GMOD codefest registration now open Message-ID: Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From ra243012 at gmail.com Tue Nov 5 13:18:58 2019 From: ra243012 at gmail.com (Robert Auber) Date: Tue, 05 Nov 2019 20:18:58 -0000 Subject: [maker-devel] Overlapping Gene Models Message-ID: Hello MAKER devs, I have been attempting to run MAKER2 (2.31.10) on an assembly of a Haptophyte genome (~160MB). After running four rounds of MAKER2 (details of pipeline shown below in diagram), I obtained a reasonable set of gene calls with great BUSCO completeness and AED scores. However, ~11,00 of the ~42,000 gene models have an overlap in their CDS with another gene model's CDS. There are no overlaps on the same strand (thank goodness), and I have read on the google group threads that cases of overlapping gene models on opposite stands can occur, but I have not seen it to this extent. Below are some examples of some overlapping models. Interestingly, some of these models have unique exon structures compared to their overlapping partner. [image: Screen Shot 2019-11-05 at 12.29.53 PM.png] [image: Screen Shot 2019-11-05 at 12.31.17 PM.png] I have tried extensively to filter out these overlapping gene models by employing different thresholds such as AED/eAED scores and amount of est/prot/etc support but the majority of these genes seem to have a minimal difference in AED scores and have multiple lines of support. The only trend I have pulled from the output is that 40% of the overlapping genes are labeled as 'snap' or 'snap processed' genes, though again most of these do have support from other sources according to the gff3. I would be very appreciative of any thought or input you may have on these overlapping gene models. If you need more metrics or information on what I did when running MAKER2 to help clarify anything, please let me know! [image: MAKER_PIPELINE_V3_maker_devs.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-11-05 at 12.29.53 PM.png Type: image/png Size: 14953 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-11-05 at 12.31.17 PM.png Type: image/png Size: 22152 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MAKER_PIPELINE_V3_maker_devs.png Type: image/png Size: 104736 bytes Desc: not available URL: From ABoyher at danforthcenter.org Fri Nov 15 14:26:13 2019 From: ABoyher at danforthcenter.org (Boyher, Adam) Date: Fri, 15 Nov 2019 21:26:13 +0000 Subject: [maker-devel] Apply old maker gff to new assembly Message-ID: Hi I'm a bit unsure of how to apply a previous maker annotation to a new assembly. I just want a quick annotation, so just taking the genes that are already in the annotation file with their functional annotations and naming schemes and find those genes in the new assembly. Which settings should i use in maker_opts.ctl? Thanks Adam From scott at scottcain.net Mon Nov 18 20:28:32 2019 From: scott at scottcain.net (Scott Cain) Date: Mon, 18 Nov 2019 19:28:32 -0800 Subject: [maker-devel] GMOD codefest registration now open Message-ID: Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From ra243012 at gmail.com Tue Nov 5 13:18:58 2019 From: ra243012 at gmail.com (Robert Auber) Date: Tue, 05 Nov 2019 20:18:58 -0000 Subject: [maker-devel] Overlapping Gene Models Message-ID: Hello MAKER devs, I have been attempting to run MAKER2 (2.31.10) on an assembly of a Haptophyte genome (~160MB). After running four rounds of MAKER2 (details of pipeline shown below in diagram), I obtained a reasonable set of gene calls with great BUSCO completeness and AED scores. However, ~11,00 of the ~42,000 gene models have an overlap in their CDS with another gene model's CDS. There are no overlaps on the same strand (thank goodness), and I have read on the google group threads that cases of overlapping gene models on opposite stands can occur, but I have not seen it to this extent. Below are some examples of some overlapping models. Interestingly, some of these models have unique exon structures compared to their overlapping partner. [image: Screen Shot 2019-11-05 at 12.29.53 PM.png] [image: Screen Shot 2019-11-05 at 12.31.17 PM.png] I have tried extensively to filter out these overlapping gene models by employing different thresholds such as AED/eAED scores and amount of est/prot/etc support but the majority of these genes seem to have a minimal difference in AED scores and have multiple lines of support. The only trend I have pulled from the output is that 40% of the overlapping genes are labeled as 'snap' or 'snap processed' genes, though again most of these do have support from other sources according to the gff3. I would be very appreciative of any thought or input you may have on these overlapping gene models. If you need more metrics or information on what I did when running MAKER2 to help clarify anything, please let me know! [image: MAKER_PIPELINE_V3_maker_devs.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-11-05 at 12.29.53 PM.png Type: image/png Size: 14953 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-11-05 at 12.31.17 PM.png Type: image/png Size: 22152 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MAKER_PIPELINE_V3_maker_devs.png Type: image/png Size: 104736 bytes Desc: not available URL: From ABoyher at danforthcenter.org Fri Nov 15 14:26:13 2019 From: ABoyher at danforthcenter.org (Boyher, Adam) Date: Fri, 15 Nov 2019 21:26:13 +0000 Subject: [maker-devel] Apply old maker gff to new assembly Message-ID: Hi I'm a bit unsure of how to apply a previous maker annotation to a new assembly. I just want a quick annotation, so just taking the genes that are already in the annotation file with their functional annotations and naming schemes and find those genes in the new assembly. Which settings should i use in maker_opts.ctl? Thanks Adam From scott at scottcain.net Mon Nov 18 20:28:32 2019 From: scott at scottcain.net (Scott Cain) Date: Mon, 18 Nov 2019 19:28:32 -0800 Subject: [maker-devel] GMOD codefest registration now open Message-ID: Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From ra243012 at gmail.com Tue Nov 5 13:18:58 2019 From: ra243012 at gmail.com (Robert Auber) Date: Tue, 05 Nov 2019 20:18:58 -0000 Subject: [maker-devel] Overlapping Gene Models Message-ID: Hello MAKER devs, I have been attempting to run MAKER2 (2.31.10) on an assembly of a Haptophyte genome (~160MB). After running four rounds of MAKER2 (details of pipeline shown below in diagram), I obtained a reasonable set of gene calls with great BUSCO completeness and AED scores. However, ~11,00 of the ~42,000 gene models have an overlap in their CDS with another gene model's CDS. There are no overlaps on the same strand (thank goodness), and I have read on the google group threads that cases of overlapping gene models on opposite stands can occur, but I have not seen it to this extent. Below are some examples of some overlapping models. Interestingly, some of these models have unique exon structures compared to their overlapping partner. [image: Screen Shot 2019-11-05 at 12.29.53 PM.png] [image: Screen Shot 2019-11-05 at 12.31.17 PM.png] I have tried extensively to filter out these overlapping gene models by employing different thresholds such as AED/eAED scores and amount of est/prot/etc support but the majority of these genes seem to have a minimal difference in AED scores and have multiple lines of support. The only trend I have pulled from the output is that 40% of the overlapping genes are labeled as 'snap' or 'snap processed' genes, though again most of these do have support from other sources according to the gff3. I would be very appreciative of any thought or input you may have on these overlapping gene models. If you need more metrics or information on what I did when running MAKER2 to help clarify anything, please let me know! [image: MAKER_PIPELINE_V3_maker_devs.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-11-05 at 12.29.53 PM.png Type: image/png Size: 14953 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-11-05 at 12.31.17 PM.png Type: image/png Size: 22152 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MAKER_PIPELINE_V3_maker_devs.png Type: image/png Size: 104736 bytes Desc: not available URL: From ABoyher at danforthcenter.org Fri Nov 15 14:26:13 2019 From: ABoyher at danforthcenter.org (Boyher, Adam) Date: Fri, 15 Nov 2019 21:26:13 +0000 Subject: [maker-devel] Apply old maker gff to new assembly Message-ID: Hi I'm a bit unsure of how to apply a previous maker annotation to a new assembly. I just want a quick annotation, so just taking the genes that are already in the annotation file with their functional annotations and naming schemes and find those genes in the new assembly. Which settings should i use in maker_opts.ctl? Thanks Adam From scott at scottcain.net Mon Nov 18 20:28:32 2019 From: scott at scottcain.net (Scott Cain) Date: Mon, 18 Nov 2019 19:28:32 -0800 Subject: [maker-devel] GMOD codefest registration now open Message-ID: Hello, As announced last month, there will be a GMOD codefest held before the Plant and Animal Genome meeting in San Diego, January 9-10, 2020. The meeting will be held at the Handlery hotel (down the street from the Town and Country Hotel). Logistical and other information can be found at the GMOD wiki as the details become more solid: http://gmod.org/wiki/Codefest_2020 Several potential projects are described in this document: https://docs.google.com/document/d/1_CnUW_W4tNyl7lSlihCwZDKT45VQQxcI3I-VgjnC2Dc/edit We know for sure that there will be developers from the Tripal, Apollo, JBrowse, and Chado projects. Of course, other projects like Galaxy, InterMine, and MAKER are welcome too! See you in San Diego! Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research -------------- next part -------------- An HTML attachment was scrubbed... URL: From ra243012 at gmail.com Tue Nov 5 13:18:58 2019 From: ra243012 at gmail.com (Robert Auber) Date: Tue, 05 Nov 2019 20:18:58 -0000 Subject: [maker-devel] Overlapping Gene Models Message-ID: Hello MAKER devs, I have been attempting to run MAKER2 (2.31.10) on an assembly of a Haptophyte genome (~160MB). After running four rounds of MAKER2 (details of pipeline shown below in diagram), I obtained a reasonable set of gene calls with great BUSCO completeness and AED scores. However, ~11,00 of the ~42,000 gene models have an overlap in their CDS with another gene model's CDS. There are no overlaps on the same strand (thank goodness), and I have read on the google group threads that cases of overlapping gene models on opposite stands can occur, but I have not seen it to this extent. Below are some examples of some overlapping models. Interestingly, some of these models have unique exon structures compared to their overlapping partner. [image: Screen Shot 2019-11-05 at 12.29.53 PM.png] [image: Screen Shot 2019-11-05 at 12.31.17 PM.png] I have tried extensively to filter out these overlapping gene models by employing different thresholds such as AED/eAED scores and amount of est/prot/etc support but the majority of these genes seem to have a minimal difference in AED scores and have multiple lines of support. The only trend I have pulled from the output is that 40% of the overlapping genes are labeled as 'snap' or 'snap processed' genes, though again most of these do have support from other sources according to the gff3. I would be very appreciative of any thought or input you may have on these overlapping gene models. If you need more metrics or information on what I did when running MAKER2 to help clarify anything, please let me know! [image: MAKER_PIPELINE_V3_maker_devs.png] -------------- next part -------------- An HTML attachment was scrubbed... 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