Quercus robur - Expression Analyses

[MattHuff]

BioProject Checklist:

---

• [x] PRJEB1903
• [x] PRJNA268569
• [x] PRJNA280092
• [x] PRJEB4873
• [x] PRJEB10691
• [x] PRJNA325588
• [x] PRJNA330761
• [x] PRJNA354688
• [x] PRJNA356360
• [x] PRJEB17875
• [x] PRJNA380755
• [x] PRJNA450334
• [x] PRJNA516042
• [x] PRJEB32849

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.

• [x] Use the python TPM script to normalize all counts files.
• [x] Load all biosamples onto the Hardwoods website.
• [x] Load the normalized counts files onto the Hardwoods website.

[MattHuff]

Some notes before starting these analyses:

• PRJEB10691 and PRJEB17875 contain three SRA files with reads taken from Quercus robur, while the other three files are derived from another Oak species that lacks a genome. Only download and analyze the three associated with Q. robur.
• Similarly, PRJNA450334 contains a mixture of different Oak species. We are only interested in the 10 SRAs obtained from Q. robur.
• PRJEB19536 only has a single SRA file associated with the project; I am figuring out whether we should lump it in with all of the other analyses, so for now ignore it.
• PRJNA479880 appears to be more related to truffles, and only a few samples are derived from Q. robur mycorrhizae. Hold off on these as well.

[CaseyRichards92]

PRJNA268569

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[patricksis]

PRJNA280092 /staton/software/sratoolkit.2.9.0-centos_linux64/bin/prefetch -v $(<acc_list.txt)

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples - Casey loaded them

[CaseyRichards92]

PRJNA380755

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA516042

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJEB4873

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJEB17875

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA356360

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [x] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA330761

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJNA325588

• [x] prefetch: 24 SRAs
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJEB10691

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[RaymondS1]

PRJEB1903

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[CaseyRichards92]

PRJNA354688

• [x] prefetch
• [x] convert to fastq
• [x] Run nextflow
• [ ] calculate tpm
• [x] Load biosamples

[MattHuff]

I have run the TPM python script on all of the files, and they are ready to be loaded onto the website. If you have biosamples that have not been loaded onto the website, now is the time to do so.

[patricksis]

All TPMs have been imported into the site: https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/876994

[CaseyRichards92]

Re-importing biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/894657

[CaseyRichards92]

Publishing biosamples https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/894658

[CaseyRichards92]

Re-importing expression data https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/894662 following guide https://github.com/mestato/statonlabprivate/wiki/Gene-Expression-Analysis-Lastest-Protocols

[CaseyRichards92]

Re-importing expression data https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/895347