Skip to content

Commit

Permalink
wip updates to workflow
Browse files Browse the repository at this point in the history
  • Loading branch information
@hexylena
hexylena committed Dec 19, 2023
1 parent 9486de8 commit 3bc9d5d
Showing 1 changed file with 141 additions and 9 deletions.
150 changes: 141 additions & 9 deletions topics/transcriptomics/tutorials/minerva-pathways/tutorial.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ tags:
- rna-seq
- viz
level: Intermediate
zenodo_link:
zenodo_link: https://zenodo.org/records/10405036
questions:
- TODO
objectives:
Expand Down Expand Up @@ -60,9 +60,7 @@ that precludes the slowest and most data intensive parts of this tutorial.
However, the entire process is documented in case you want to reproduce our
work.

# Data upload

TODO
## Study Design

> <hands-on-title>Data upload</hands-on-title>
>
Expand Down Expand Up @@ -144,20 +142,154 @@ TODO
>
{: .hands_on}

## Data Download

## Analysis

We have split this workflow into two parts, based only on how long the first portion of the workflow takes to execute. The rough runtime of the workflow portions when this was being developed can be broken down as follows:

Step | Time
--- | ---
Data Download | ~6h
Processing Counts | ~8h
Analysis & Visualisation | 15m

These numbers were generated on UseGalaxy.eu and may not represent the most
efficient possible computation, as they are executed on a shared cluster that can, at times, be more or less busy.

As such we recommend you skip to [Limma](#limma) to progress to the efficient
portion. The data provided in the Zenodo record is from the entire analysis,
analysed with the Counts step that can be skipped:

### Counts

# Analysis
We'll start by downloading our fastq files from the [GEO Dataset GSE182152](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE182152)

## limma
> <hands-on-title>Download the data from GEO (ETA: 6 Hours)</hands-on-title>
>
> 1. {% tool [Cut](Cut1) %} with the following parameters:
> - *"Cut columns"*: `c1`
> - {% icon param-file %} *"Select lines from"*: `factordata`
>
> 1. {% tool [Select](Grep1) %} with the following parameters:
> - {% icon param-file %} *"Select lines from"*: `out_file1` (output of **Cut** {% icon tool %})
> - *"that"*: `NOT Matching`
> - *"the pattern"*: `Run`
>
> 1. {% tool [Faster Download and Extract Reads in FASTQ](toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/3.0.8+galaxy1) %} with the following parameters:
> - *"select input type"*: `List of SRA accession, one per line`
> - {% icon param-file %} *"sra accession list"*: `out_file1` (output of **Select** {% icon tool %})
>
{: .hands_on}

With the
With that done, we can start to analyse the data using HISAT2 and featureCounts

> <hands-on-title>Run the Workflow</hands-on-title>
>
> 1. **Import the workflow** into Galaxy
>
> {% snippet faqs/galaxy/workflows_run_wfh.md title="mRNA-Seq BY-COVID Pipeline" wfhub_id="685" %}
> {% snippet faqs/galaxy/workflows_run_wfh.md title="mRNA-Seq BY-COVID Pipeline" wfhub_id="688" %}
>
> Provide the factor data, RNA Sequencing data, and annotations files to the appropriate fields.
{: .hands_on}

This workflow produces a handful of outputs: the featureCounts results, and a
MultiQC report. Looking at the report we see generally reasonable quality data.

### limma

> <hands-on-title>Only If You Skipped Here: Download the Counts Files</hands-on-title>
>
> 1. Open the Rule Builder
> - *"Upload data as"*: `Collection(s)`
> - *"Load tabular data from"*: `Pasted Table`
> - **Paste** the following table:
>
> ```
> https://zenodo.org/records/10405036/files/gene_lengths.tabular gene_lengths Gene Lengths
> https://zenodo.org/records/10405036/files/SRR15462516.featureCounts.tabular SRR15462516 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462517.featureCounts.tabular SRR15462517 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462518.featureCounts.tabular SRR15462518 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462519.featureCounts.tabular SRR15462519 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462520.featureCounts.tabular SRR15462520 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462521.featureCounts.tabular SRR15462521 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462522.featureCounts.tabular SRR15462522 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462523.featureCounts.tabular SRR15462523 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462524.featureCounts.tabular SRR15462524 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462525.featureCounts.tabular SRR15462525 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462526.featureCounts.tabular SRR15462526 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462527.featureCounts.tabular SRR15462527 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462528.featureCounts.tabular SRR15462528 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462529.featureCounts.tabular SRR15462529 featureCounts
> https://zenodo.org/records/10405036/files/SRR15462530.featureCounts.tabular SRR15462530 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681520.featureCounts.tabular SRR16681520 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681521.featureCounts.tabular SRR16681521 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681522.featureCounts.tabular SRR16681522 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681523.featureCounts.tabular SRR16681523 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681524.featureCounts.tabular SRR16681524 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681525.featureCounts.tabular SRR16681525 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681526.featureCounts.tabular SRR16681526 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681527.featureCounts.tabular SRR16681527 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681528.featureCounts.tabular SRR16681528 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681529.featureCounts.tabular SRR16681529 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681530.featureCounts.tabular SRR16681530 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681531.featureCounts.tabular SRR16681531 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681532.featureCounts.tabular SRR16681532 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681533.featureCounts.tabular SRR16681533 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681534.featureCounts.tabular SRR16681534 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681535.featureCounts.tabular SRR16681535 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681536.featureCounts.tabular SRR16681536 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681537.featureCounts.tabular SRR16681537 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681538.featureCounts.tabular SRR16681538 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681539.featureCounts.tabular SRR16681539 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681540.featureCounts.tabular SRR16681540 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681541.featureCounts.tabular SRR16681541 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681542.featureCounts.tabular SRR16681542 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681543.featureCounts.tabular SRR16681543 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681544.featureCounts.tabular SRR16681544 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681545.featureCounts.tabular SRR16681545 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681546.featureCounts.tabular SRR16681546 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681547.featureCounts.tabular SRR16681547 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681548.featureCounts.tabular SRR16681548 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681549.featureCounts.tabular SRR16681549 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681550.featureCounts.tabular SRR16681550 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681551.featureCounts.tabular SRR16681551 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681552.featureCounts.tabular SRR16681552 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681553.featureCounts.tabular SRR16681553 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681554.featureCounts.tabular SRR16681554 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681555.featureCounts.tabular SRR16681555 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681556.featureCounts.tabular SRR16681556 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681557.featureCounts.tabular SRR16681557 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681558.featureCounts.tabular SRR16681558 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681559.featureCounts.tabular SRR16681559 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681560.featureCounts.tabular SRR16681560 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681561.featureCounts.tabular SRR16681561 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681562.featureCounts.tabular SRR16681562 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681563.featureCounts.tabular SRR16681563 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681564.featureCounts.tabular SRR16681564 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681565.featureCounts.tabular SRR16681565 featureCounts
> https://zenodo.org/records/10405036/files/SRR16681566.featureCounts.tabular SRR16681566 featureCounts
> ```
>
> - Click `Build`
>
> 1. From **Rules** menu, select `Add / Modify Column Definitions`
> - `Add Definition`, `Collection Name`, Select Column `C`
> - `Add Definition`, `List Identifier(s)`, Select Column `B`
> - `Add Definition`, `URL`, Column `A`
>
{: .hands_on}


> <hands-on-title>Analyse the Counts</hands-on-title>
>
> 1. Run the workflow with the Factor Data from the first Hands on, and the datasets from the workflow or Zenodo download, depending on your path:
>
> {% snippet faqs/galaxy/workflows_run_wfh.md title="mRNA-Seq BY-COVID Pipeline" wfhub_id="689" %}
>
{: .hands_on}

You should have a few outputs, namely the `goseq` outputs, and a table ready for visualisation in MINERVA!

## MINERVA

TODO

0 comments on commit 3bc9d5d

Please sign in to comment.