Quercus robur DF159 - Expression Data

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues

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Quercus robur DF159 - Expression Data #551

Open MattHuff opened 4 years ago

MattHuff commented 4 years ago

Publication and Data Information

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA516042

Additional Information

Checklist

See New Genome Documentation for detailed instructions.

[x] Run Nextflow Script to get counts.txt files.
[x] Run Python Script to normalize counts with TPM.
[ ] Load normalized counts onto Hardwoods site.
[ ] Run DESeq2 on raw counts files, obtain p-values.
[ ] Load p-values onto Hardwoods site.

CaseyRichards92 commented 4 years ago

Analysis created https://www.hardwoodgenomics.org/Analysis/3958590

CaseyRichards92 commented 4 years ago

Various scripts /staton/software/sratoolkit.2.9.0-centos_linux64/bin/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files * /staton/software/sratoolkit.2.9.0-centos_linux64/bin/prefetch -v $(<SraAccList.txt) /staton/software/sratoolkit.2.9.0-centos_linux64/bin/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files $S*.sra python /staton/unpublished_lab_code/python/calculate_tpm.py /staton/projects/undergrads/quercus_robur/oak_gene_casey/Qrob_PM1N_CDS_nt_20161004.fa /staton/projects/undergrads/quercus_robur_df159/analysis/3_htseq/

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

Biosamples not loading correctly Properties not configured. Using generic cvterms for all properties. File is not readable or not present. https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/866273

CaseyRichards92 commented 4 years ago

Expression data loader test https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/866277

CaseyRichards92 commented 4 years ago

There are multiple instance of the following feature(s) in the expression file: Qrob_P0000020.2 Please make sure there is only one instance of each feature in the expression file.

Done.

CaseyRichards92 commented 4 years ago

Trying biosamples w/ xml rather than a tsv https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/866278

CaseyRichards92 commented 4 years ago

Received:

Properties not configured. Using generic cvterms for all properties. XML must contain a BioSample tag. Check your XML file and try again.

Done.

Biosamples are present when opening the xml

CaseyRichards92 commented 4 years ago

Trying with a .csv https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/866279

CaseyRichards92 commented 4 years ago

Getting closer...