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

Prunus persica - Expression Analyses #575

Open
20 of 21 tasks
MattHuff opened this issue Apr 13, 2020 · 19 comments
Open
20 of 21 tasks

Prunus persica - Expression Analyses #575

MattHuff opened this issue Apr 13, 2020 · 19 comments
Assignees
@patricksis @CaseyRichards92 @RaymondS1
Labels
data upload Load into Chado Undergraduate Task

Comments

@MattHuff
Copy link

MattHuff commented Apr 13, 2020 •
edited by patricksis
Loading

BioProject Checklist:

  • PRJNA526626
  • PRJNA474565
  • PRJNA448600
  • PRJNA439260
  • PRJNA567655 - Only use the 69 samples from Prunus persica
  • PRJEB12334
  • PRJNA454883
  • PRJNA388577
  • PRJNA382313
  • PRJNA353968
  • PRJNA323761 - Only use the 7 samples from Prunus persica
  • PRJNA314683
  • PRJNA268256
  • PRJNA260463
  • PRJNA252780
  • PRJNA248711
  • PRJNA612533
  • PRJDB4505

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.
@patricksis
Copy link

patricksis commented May 11, 2020 •
edited
Loading

PRJNA474565

  • fastq_dump (6 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

1 similar comment
@patricksis
Copy link

patricksis commented May 12, 2020 •
edited
Loading

PRJNA474565

  • fastq_dump (6 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented May 27, 2020 •
edited
Loading

PRJNA526626

  • fastq_dump (16 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples
    Issue with STAR not mapping to genome
    We're trashing this one, reads are just bad

@patricksis
Copy link

patricksis commented May 27, 2020 •
edited
Loading

PRJNA448600

  • fastq_dump (8 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented May 28, 2020 •
edited
Loading

PRJNA439260

  • fastq_dump (8 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented May 28, 2020 •
edited
Loading

PRJNA567655

  • fastq_dump (69 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jun 3, 2020 •
edited
Loading

PRJNA454883

  • fastq_dump (32 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jun 4, 2020 •
edited
Loading

PRJNA388577

  • fastq_dump (32 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jun 29, 2020 •
edited
Loading

PRJNA382313

  • fastq_dump (12 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jul 1, 2020 •
edited
Loading

PRJNA323761

  • fastq_dump (7 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jul 5, 2020 •
edited
Loading

PRJNA314683

  • fastq_dump (7 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jul 5, 2020 •
edited
Loading

PRJNA268256

  • fastq_dump (2 SRAs)
    * Error prefetch.2.9.0: 'SRR1662174' has no remote vdbcache on prefetch
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jul 6, 2020 •
edited
Loading

PRJNA323761

  • fastq_dump (7 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

PRJNA260463

  • fastq_dump (6 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jul 6, 2020 •
edited
Loading

PRJNA252780

  • fastq_dump (3 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

PRJNA248711

  • fastq_dump (5 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jul 10, 2020 •
edited
Loading

PRJNA612533

  • fastq_dump (73 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

patricksis commented Jul 24, 2020 •
edited
Loading

PRJDB4505

  • fastq_dump (3 SRAs)
  • Run nextflow
  • calculate tpm
  • Load biosamples

@patricksis
Copy link

Biosample loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903619

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