From christopher.keeling.1 at ulaval.ca Tue Jul 7 18:12:59 2020 From: christopher.keeling.1 at ulaval.ca (Christopher Keeling) Date: Wed, 08 Jul 2020 00:12:59 -0000 Subject: [maker-devel] Maker 2.31.10: maker_functional_gff and maker_functional_fasta not parsing correctly, Can't use string ("") as a HASH ref while "strict refs" in use In-Reply-To: <4A449297-A6D1-4A75-9547-FB5F70CE1A0A@ulaval.ca> References: <4A449297-A6D1-4A75-9547-FB5F70CE1A0A@ulaval.ca> Message-ID: <49E0078D-C779-4D0D-ADF2-13E524E27EE5@ulaval.ca> An HTML attachment was scrubbed... URL: From wei.xiong at wur.nl Fri Jul 24 03:04:43 2020 From: wei.xiong at wur.nl (Xiong, Wei) Date: Fri, 24 Jul 2020 09:04:43 +0000 Subject: [maker-devel] protein homology evidence Message-ID: Dear colleague, I couldn't find a related answer online for the following question that might sound silly. If I want to include protein homology evidence from multiple species, what should I do? Can I directly merge the protein sequence files of different species and feed it to MAKER? Thank you for your help in advance. I look forward to hearing from you. I wish you a pleasant and healthy summer! Met vriendelijke groet, With kind regards, Wei Xiong PhD candidate | Wageningen University & Research Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands E-mail: wei.xiong at wur.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Jul 26 23:31:22 2020 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 27 Jul 2020 06:31:22 +0100 Subject: [maker-devel] Maker Snap annotation yields match_part Message-ID: Hello, I am annotating my genome using SNAP after running SNAP twice my GFF has quite a number of match_part. How can I get an actual match? ilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 890 1003 +;Gap=M114 contig_844_pilon_pilon_pilon snap_masked match_part 66719 66729 8.644 + . ID=contig_844_pilon_pilon_pilon:hsp:2866471:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 1004 1014 +;Gap=M11 Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: From christopher.keeling.1 at ulaval.ca Tue Jul 7 18:12:59 2020 From: christopher.keeling.1 at ulaval.ca (Christopher Keeling) Date: Wed, 08 Jul 2020 00:12:59 -0000 Subject: [maker-devel] Maker 2.31.10: maker_functional_gff and maker_functional_fasta not parsing correctly, Can't use string ("") as a HASH ref while "strict refs" in use In-Reply-To: <4A449297-A6D1-4A75-9547-FB5F70CE1A0A@ulaval.ca> References: <4A449297-A6D1-4A75-9547-FB5F70CE1A0A@ulaval.ca> Message-ID: <49E0078D-C779-4D0D-ADF2-13E524E27EE5@ulaval.ca> An HTML attachment was scrubbed... URL: From wei.xiong at wur.nl Fri Jul 24 03:04:43 2020 From: wei.xiong at wur.nl (Xiong, Wei) Date: Fri, 24 Jul 2020 09:04:43 +0000 Subject: [maker-devel] protein homology evidence Message-ID: Dear colleague, I couldn't find a related answer online for the following question that might sound silly. If I want to include protein homology evidence from multiple species, what should I do? Can I directly merge the protein sequence files of different species and feed it to MAKER? Thank you for your help in advance. I look forward to hearing from you. I wish you a pleasant and healthy summer! Met vriendelijke groet, With kind regards, Wei Xiong PhD candidate | Wageningen University & Research Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands E-mail: wei.xiong at wur.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Jul 26 23:31:22 2020 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 27 Jul 2020 06:31:22 +0100 Subject: [maker-devel] Maker Snap annotation yields match_part Message-ID: Hello, I am annotating my genome using SNAP after running SNAP twice my GFF has quite a number of match_part. How can I get an actual match? ilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 890 1003 +;Gap=M114 contig_844_pilon_pilon_pilon snap_masked match_part 66719 66729 8.644 + . ID=contig_844_pilon_pilon_pilon:hsp:2866471:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 1004 1014 +;Gap=M11 Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: From christopher.keeling.1 at ulaval.ca Tue Jul 7 18:12:59 2020 From: christopher.keeling.1 at ulaval.ca (Christopher Keeling) Date: Wed, 08 Jul 2020 00:12:59 -0000 Subject: [maker-devel] Maker 2.31.10: maker_functional_gff and maker_functional_fasta not parsing correctly, Can't use string ("") as a HASH ref while "strict refs" in use In-Reply-To: <4A449297-A6D1-4A75-9547-FB5F70CE1A0A@ulaval.ca> References: <4A449297-A6D1-4A75-9547-FB5F70CE1A0A@ulaval.ca> Message-ID: <49E0078D-C779-4D0D-ADF2-13E524E27EE5@ulaval.ca> An HTML attachment was scrubbed... URL: From wei.xiong at wur.nl Fri Jul 24 03:04:43 2020 From: wei.xiong at wur.nl (Xiong, Wei) Date: Fri, 24 Jul 2020 09:04:43 +0000 Subject: [maker-devel] protein homology evidence Message-ID: Dear colleague, I couldn't find a related answer online for the following question that might sound silly. If I want to include protein homology evidence from multiple species, what should I do? Can I directly merge the protein sequence files of different species and feed it to MAKER? Thank you for your help in advance. I look forward to hearing from you. I wish you a pleasant and healthy summer! Met vriendelijke groet, With kind regards, Wei Xiong PhD candidate | Wageningen University & Research Plant Science Group | Biosystematics Group Radix Building 107 Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands E-mail: wei.xiong at wur.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From eennadi at gmail.com Sun Jul 26 23:31:22 2020 From: eennadi at gmail.com (Emmanuel Nnadi) Date: Mon, 27 Jul 2020 06:31:22 +0100 Subject: [maker-devel] Maker Snap annotation yields match_part Message-ID: Hello, I am annotating my genome using SNAP after running SNAP twice my GFF has quite a number of match_part. How can I get an actual match? ilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 890 1003 +;Gap=M114 contig_844_pilon_pilon_pilon snap_masked match_part 66719 66729 8.644 + . ID=contig_844_pilon_pilon_pilon:hsp:2866471:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2447078:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 1004 1014 +;Gap=M11 Nnadi Nnaemeka Emmanuel,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications: https://www.researchgate.net/profile/Emmanuel_Nnadi/publications -------------- next part -------------- An HTML attachment was scrubbed... URL: