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statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues
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Oak gene expression atlas #537

Open mestato opened 5 years ago

mestato commented 5 years ago

Publication and Data Information

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1331-9

Additional Information

Seems to have two species, possibly assembled as a single transcriptome. May have to create a hybrid organism to hold the data.

Checklist

See New Genome Documentation for detailed instructions.

CaseyRichards92 commented 5 years ago

Data was obtained from pub. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-650

Accession #: SRA012448

Leads to a project about a fruit fly and not quercus. May have been loaded incorrectly by author.

CaseyRichards92 commented 5 years ago

Oak ( Quercus petraea and Q. robur ) cDNA libraries used for Sanger, 454 Roche and Illumina sequencing.

https://static-content.springer.com/esm/art%3A10.1186%2Fs12864-015-1331-9/MediaObjects/12864_2015_1331_MOESM1_ESM.xls

CaseyRichards92 commented 4 years ago

In the GFF file 23 lines contained this "Note=Gene manually annotated in v1 and curated after mapping because stop in CDS;" Which caused HTSeq to fail. Removed all instances of the string in the gff.

CaseyRichards92 commented 4 years ago

Genes that were manually updated are causing issues when running htseq. There is no information on gene ID, only "Name=...", and the source is changed from "egn" to "Manual_v2." Should we continue with this project by removing the manually annotated genes or move on to another project?

CaseyRichards92 commented 4 years ago

Expression Analysis created https://www.hardwoodgenomics.org/Analysis/3930251

CaseyRichards92 commented 4 years ago

Import tripal epression data job https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/847204

CaseyRichards92 commented 4 years ago

Publication added to expression analysis https://www.hardwoodgenomics.org/Publication/3930252

CaseyRichards92 commented 4 years ago

@almasaeed2010 @MattHuff Import tripal epression data job continues to terminate unexpectedly https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/847211

CaseyRichards92 commented 4 years ago

Added tpm into the "File Suffix Type" field and re ran job https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/849626

almasaeed2010 commented 4 years ago

Populating expression views

https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/849628

CaseyRichards92 commented 4 years ago

Had to change the T back to P so they would match with the genes and re ran the job https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/853530

CaseyRichards92 commented 4 years ago

Re-ran expression job https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/861776

CaseyRichards92 commented 4 years ago

Expression job completed but genes expression data not appearing on hardwoods. https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/863571 https://www.hardwoodgenomics.org/content/expression-visualization?heatmap_feature_uniquename=Qrob_P0121800.2%2CQrob_P0281650.2&op=Display+Expression+Heatmap&form_build_id=form-2enNMhBJvUmiIXHHdRm1LiVtkj3KKZGjssP8uwiJaPw&form_token=THPTpLv6V9h4neLl3-bHGlsJokFTaCJ9mQH41ZTnjR0&form_id=feature_heatmap_form

CaseyRichards92 commented 4 years ago

Need to do biosamples https://tripal-devseed.readthedocs.io/en/latest/loading_biosamples.html

CaseyRichards92 commented 4 years ago

Bio samples job https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/866826