Malus domestica - expression analyses

[MattHuff]

BioProject Checklist:

---

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

PRJNA549565

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

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

[CaseyRichards92]

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

[CaseyRichards92]

PRJNA507638

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJNA357091

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJNA505541

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA480546

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJNA480110

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJNA419119

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA374502

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA362843

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJNA349086

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA348828

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJNA339488

• [x] fastq_dump
• [ ] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJNA327898

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA311518

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA308148

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA306594

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJNA299491

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJNA264060

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJNA263198

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJNA599090

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

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]

PRJEB4314

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJEB12104

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJDB6779

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[RaymondS1]

PRJDB6779

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

PRJDB4784

• [x] fastq_dump
• [x] Run nextflow
• [ ] calculate tpm
• [ ] Load biosamples

[CaseyRichards92]

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

[CaseyRichards92]

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