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  1. IGB
  2. IGBF-2333

Add wheat genome to IGB quickload system

        Details

        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct

          Description

          We received a request to wheat genome to IGB Quickload.

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              Issue Links

              relates to

              New Feature - A new feature of the product, which has yet to be developed. IGBF-2541 Add wheat genome image to genome dashboard

              • Major - Major loss of function.
              • Closed

              New Feature - A new feature of the product, which has yet to be developed. HELP-337 Add wheat genome to IGB

              • Major - Major loss of function.
              • To-Do

              New Feature - A new feature of the product, which has yet to be developed. IGBF-2538 Support CSI tabix index for very large genomes

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-2548 Investigate: Why do wheat gene models fail to load

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3409 Fix wheat genome files and documentation

              • Major - Major loss of function.
              • To-Do

              New Feature - A new feature of the product, which has yet to be developed. IGBF-2538 Support CSI tabix index for very large genomes

              • Major - Major loss of function.
              • To-Do

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Link This issue relates to HELP-337 [ HELP-337 ]
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                ann.loraine Ann Loraine added a comment -

                Bread wheat genome

                Int Wheat Genome Sequencing Consortium https://www.wheatgenome.org/News/Latest-news/All-IWGSC-data-related-to-the-reference-sequence-of-bread-wheat-IWGSC-RefSeq-v1.0-publicly-available-at-URGI

                https://plants.ensembl.org/Triticum_aestivum/Info/Index

                (These links are all for the RefSeq v1.0 version, which is most widely accepted and used today in the community)

                Only last week released T4 genome (but based on the IWGSC work):

                https://www.ncbi.nlm.nih.gov/bioproject/PRJNA392179

                https://www.biorxiv.org/content/10.1101/2020.04.06.028746v1.full.pdf

                Durum wheat genome

                https://www.interomics.eu/durum-wheat-genome

                http://plants.ensembl.org/Triticum_turgidum/Info/Index

                wheat training (Small summary from our group about the wheat genome assemblies) http://www.wheat-training.com/wp-content/uploads/Genomic_resources/pdfs/Genome_assemblies.pdf

                Show
                ann.loraine Ann Loraine added a comment - Bread wheat genome Int Wheat Genome Sequencing Consortium https://www.wheatgenome.org/News/Latest-news/All-IWGSC-data-related-to-the-reference-sequence-of-bread-wheat-IWGSC-RefSeq-v1.0-publicly-available-at-URGI https://plants.ensembl.org/Triticum_aestivum/Info/Index (These links are all for the RefSeq v1.0 version, which is most widely accepted and used today in the community) Only last week released T4 genome (but based on the IWGSC work): https://www.ncbi.nlm.nih.gov/bioproject/PRJNA392179 https://www.biorxiv.org/content/10.1101/2020.04.06.028746v1.full.pdf Durum wheat genome https://www.interomics.eu/durum-wheat-genome http://plants.ensembl.org/Triticum_turgidum/Info/Index wheat training (Small summary from our group about the wheat genome assemblies) http://www.wheat-training.com/wp-content/uploads/Genomic_resources/pdfs/Genome_assemblies.pdf
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr [ 92 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 92, 93 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May [ 92, 93 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 92, 93, 94 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May [ 92, 93, 94 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 92, 93, 94, 95 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun [ 92, 93, 94, 95 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 92, 93, 94, 95, 96 ]
                ann.loraine Ann Loraine made changes -
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                ann.loraine Ann Loraine made changes -
                Labels Advanced
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun [ 92, 93, 94, 95, 96 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 July [ 92, 93, 94, 95, 96, 97 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul [ 92, 93, 94, 95, 96, 97 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 3 Jul - 14 Jul [ 92, 93, 94, 95, 96, 97, 98 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul [ 92, 93, 94, 95, 96, 97, 98 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul [ 92, 93, 94, 95, 96, 97, 98, 99 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul [ 92, 93, 94, 95, 96, 97, 98, 99 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 29 Jul - 12 Aug [ 92, 93, 94, 95, 96, 97, 98, 99, 100 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug [ 92, 93, 94, 95, 96, 97, 98, 99, 100 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
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                ann.loraine Ann Loraine added a comment - - edited

                Downloaded bread wheat genome from Ensembl. Fixed headers with:

                sed 's| dna_sm:chromosome chromosome:IWGSC:..:1:.*:1 REF||

                IGB name for bread wheat genome version 1 is T_aestivum_Aug_2018.
                Looked for wheat in https://usegalaxy.org/api/genomes (galaxy-supported genomes) but did not find it.
                A new version 2 is coming soon but not yet publicly available for redistribution in IGB Quickload.
                Converted fasta file is 2bit file of size is 3.6 Gb.
                Converted from: Triticum_aestivum.IWGSC.dna_sm.toplevel.fa, downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna_sm.toplevel.fa.gz.
                Saved 2bit file in /nobackup at UNCC cluster.
                Wrote new code for parsing ensembl gff.

                Show
                ann.loraine Ann Loraine added a comment - - edited Downloaded bread wheat genome from Ensembl. Fixed headers with: sed 's| dna_sm:chromosome chromosome:IWGSC:..:1:.*:1 REF|| IGB name for bread wheat genome version 1 is T_aestivum_Aug_2018. Looked for wheat in https://usegalaxy.org/api/genomes (galaxy-supported genomes) but did not find it. A new version 2 is coming soon but not yet publicly available for redistribution in IGB Quickload. Converted fasta file is 2bit file of size is 3.6 Gb. Converted from: Triticum_aestivum.IWGSC.dna_sm.toplevel.fa, downloaded from ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna_sm.toplevel.fa.gz . Saved 2bit file in /nobackup at UNCC cluster. Wrote new code for parsing ensembl gff.
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2538 [ IGBF-2538 ]
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                ann.loraine Ann Loraine added a comment -

                Bread wheat genome is too large for .bai and .tbi indexes.
                Need to support .csi indexes.

                Show
                ann.loraine Ann Loraine added a comment - Bread wheat genome is too large for .bai and .tbi indexes. Need to support .csi indexes.
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                ann.loraine Ann Loraine added a comment -

                Added csi-index and bgzip sorted BED file to quickload. Did not add genome 2bit to the svn repo because it is too big - 3.9 Gb.
                igbquickload.org host is down. Updated sci-das server and ec2 server.

                Show
                ann.loraine Ann Loraine added a comment - Added csi-index and bgzip sorted BED file to quickload. Did not add genome 2bit to the svn repo because it is too big - 3.9 Gb. igbquickload.org host is down. Updated sci-das server and ec2 server.
                ann.loraine Ann Loraine made changes -
                Attachment wheat.png [ 14876 ]
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                ann.loraine Ann Loraine added a comment -

                Attached image shows newly added wheat genome.

                Show
                ann.loraine Ann Loraine added a comment - Attached image shows newly added wheat genome.
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2541 [ IGBF-2541 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
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                nfreese Nowlan Freese added a comment -

                Tested on mac with IGB 9.1.6 (Sept 24 master).

                When I load the Triticum aestivum genome in IGB the gene annotations are loading for some chromosomes but not others. If I uncheck the IGB Quickload Gene models and then re-select it and change Load Mode to Genome all of the chromosome gene models load correctly.

                This may have to do with the annotations not being tabix indexed, due to the large size of the wheat chromosomes.

                Show
                nfreese Nowlan Freese added a comment - Tested on mac with IGB 9.1.6 (Sept 24 master). When I load the Triticum aestivum genome in IGB the gene annotations are loading for some chromosomes but not others. If I uncheck the IGB Quickload Gene models and then re-select it and change Load Mode to Genome all of the chromosome gene models load correctly. This may have to do with the annotations not being tabix indexed, due to the large size of the wheat chromosomes.
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103 ] Spring 7 : 13 Apr to 24 Apr, Spring 8 : 24 Apr to 8 May, Spring 8 : 11 May to 25 May, Spring 9 : 25 May to 8 Jun, Summer 1: 8 Jun - 19 Jun, Summer 2: 22 Jun - 3 Jul, Summer 3: 6 Jul - 17 Jul, Summer 4: 14 Jul - 28 Jul, Summer 5: 3 Aug - 14 Aug, Summer 6: 17 Aug - 28 Aug, Summer 7: 31 Aug - 11 Sep, Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2538 [ IGBF-2538 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2548 [ IGBF-2548 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Fix Version/s 9.1.6 Major Release [ 10604 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3409 [ IGBF-3409 ]

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                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: