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  1. IGB
  2. IGBF-2333

Add wheat genome to IGB quickload system

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        • 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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              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

              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

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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

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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
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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.

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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.
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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.

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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.
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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.
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                ann.loraine Ann Loraine added a comment -

                Attached image shows newly added wheat genome.

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                ann.loraine Ann Loraine added a comment - Attached image shows newly added wheat genome.
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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.

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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.

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                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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