Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Juglans regia - expression analyses #594

Open
7 of 10 tasks
MattHuff opened this issue Jul 6, 2020 · 9 comments
Open
7 of 10 tasks

Juglans regia - expression analyses #594

MattHuff opened this issue Jul 6, 2020 · 9 comments
Assignees
@patricksis @CaseyRichards92 @RaymondS1
Labels
data upload Load into Chado Undergraduate Task

Comments

@MattHuff
Copy link

MattHuff commented Jul 6, 2020 •
edited by CaseyRichards92
Loading

BioProject Checklist:

  • PRJNA335887
  • PRJNA319865
  • PRJNA272975
  • PRJNA235890
  • PRJNA237044
  • PRJNA232394
  • PRJNA613956

Follow the Gene Expression Protocols on each of the SRAs in each Bioproject, but do not run TPM normalization on them until the pipeline has been run on all BioProjects.

  • Use the python TPM script to normalize all counts files.
  • Load all biosamples onto the Hardwoods website.
  • Load the normalized counts files onto the Hardwoods website.
@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 9, 2020 •
edited
Loading

Waitin response from ACF due to genome indexing failure error

Jul 09 13:45:28 ..... started STAR run
Jul 09 13:45:28 ... starting to generate Genome files
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted

ppn increased to 8 resolved issue

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 10, 2020 •
edited
Loading

PRJNA335887

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 14, 2020 •
edited
Loading

PRJNA319865

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 14, 2020 •
edited
Loading

PRJNA272975

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 15, 2020 •
edited
Loading

PRJNA235890

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 15, 2020 •
edited
Loading

PRJNA237044

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 16, 2020 •
edited
Loading

PRJNA232394

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 16, 2020 •
edited
Loading

PRJNA613956

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

Gene atlas https://hardwoodgenomics.org/Gene-expression-profiling/4210013
Biosample loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899707
Published Biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899711
Expression data loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899712

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@patricksis patricksis

@CaseyRichards92 CaseyRichards92

@RaymondS1 RaymondS1

Labels
data upload Load into Chado Undergraduate Task
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@MattHuff @patricksis @CaseyRichards92 @RaymondS1