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

Malus domestica - expression analyses #576

Open
25 of 28 tasks
MattHuff opened this issue Apr 15, 2020 · 30 comments
Open
25 of 28 tasks

Malus domestica - expression analyses #576

MattHuff opened this issue Apr 15, 2020 · 30 comments
Assignees
@patricksis @CaseyRichards92 @RaymondS1
Labels
data upload Load into Chado Undergraduate Task

Comments

@MattHuff
Copy link

MattHuff commented Apr 15, 2020 •
edited by CaseyRichards92
Loading

BioProject Checklist:

  • PRJNA549565
  • PRJNA357091
  • PRJNA507638
  • PRJNA505541
  • PRJNA480546
  • PRJNA480110
  • PRJNA419119
  • PRJNA374502
  • PRJNA362843
  • PRJNA349086
  • PRJNA348828
  • PRJNA339488
  • PRJNA327898
  • PRJNA311518
  • PRJNA308148
  • PRJNA306594
  • PRJNA299491
  • PRJNA264060
  • PRJNA263198
  • PRJNA599090
  • PRJEB1902
  • PRJEB4314
  • PRJEB12104
  • PRJDB6779
  • PRJDB4784

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 Apr 20, 2020 •
edited
Loading

PRJNA549565

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

Organism created https://hardwoodgenomics.org/organism/Malus/domestica?tripal_pane=group_summary_tripalpane

@CaseyRichards92
Copy link

Analysis for biosamples https://hardwoodgenomics.org/Analysis/3959606

@CaseyRichards92
Copy link

CaseyRichards92 commented May 12, 2020 •
edited
Loading

PRJNA507638

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented May 18, 2020 •
edited
Loading

PRJNA357091

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented May 18, 2020 •
edited
Loading

PRJNA505541

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented May 19, 2020 •
edited
Loading

PRJNA480546

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented May 25, 2020 •
edited
Loading

PRJNA480110

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented May 25, 2020 •
edited
Loading

PRJNA419119

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented May 26, 2020 •
edited
Loading

PRJNA374502

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented May 27, 2020 •
edited
Loading

PRJNA362843

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jun 1, 2020 •
edited
Loading

PRJNA349086

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 1, 2020 •
edited
Loading

PRJNA348828

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jun 2, 2020 •
edited
Loading

PRJNA339488

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jun 2, 2020 •
edited
Loading

PRJNA327898

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 3, 2020 •
edited
Loading

PRJNA311518

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 4, 2020 •
edited
Loading

PRJNA308148

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 5, 2020 •
edited
Loading

PRJNA306594

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jun 8, 2020 •
edited
Loading

PRJNA299491

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jun 8, 2020 •
edited
Loading

PRJNA264060

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@RaymondS1
Copy link

RaymondS1 commented Jun 8, 2020 •
edited
Loading

PRJNA263198

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 9, 2020 •
edited
Loading

PRJNA599090

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 19, 2020 •
edited
Loading

PRJEB1902

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

Receiving error on ACF

2020-06-22T15:52:11 fastq-dump.2.9.0 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )
2020-06-22T15:52:19 fastq-dump.2.9.0 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )
2020-06-22T15:52:47 fastq-dump.2.9.0 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )
2020-06-22T15:52:50 fastq-dump.2.9.0 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )```

Receiving error on Staton Server

```2020-06-22T15:53:15 fastq-dump.2.10.3 err: connection not found while validating within network system module - error with https open 'https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/ERR493373/ERR493373.1'
2020-06-22T15:53:15 fastq-dump.2.10.3 err: item not found while constructing within virtual database module - the path 'ERR493373' cannot be opened as database or table
fastq-dump (PID 118950) quit with error code 3```

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 22, 2020 •
edited
Loading

PRJEB4314

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 23, 2020 •
edited
Loading

PRJEB12104

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jun 24, 2020 •
edited
Loading

PRJDB6779

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

1 similar comment
@RaymondS1
Copy link

RaymondS1 commented Jun 29, 2020 •
edited
Loading

PRJDB6779

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 2, 2020 •
edited
Loading

PRJDB4784

  • fastq_dump
  • Run nextflow
  • calculate tpm
  • Load biosamples

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 20, 2020 •
edited
Loading

Biosample loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/897672
Published biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/897673

@CaseyRichards92
Copy link

CaseyRichards92 commented Jul 20, 2020 •
edited
Loading

Gene expression loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/897680

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