Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:3
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Epic Link:
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Sprint:Summer 1
Description
GOAL:
To use the newly annotated Trinity files as a REFERENCE to align reads to and determine gene expression for Kelsey's dataset.
There are 4 newly generated Trinity sets of contigs (TMNH). See IGBF-3741.
Want to run NEXTFLOW. One for each variety.
Location of Trinity COntigs:
/projects/tomato_genome/fnb/dataprocessing/trinity/NEXTFLOW/postblat
(there should be 4 fasta files here, if not yet, soon.....)
The reads that will be used are here:
/projects/tomato_genome/rnaseq/renamed_Ravi_Combined
Instead of running ALL reads, we be separating by variety.
So only using the reads fr heinz with the Heinz trinity contig file......
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Ann Loraine [ aloraine ] | Robert Reid [ robertreid ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Need all the pieces for next flow:
- A csv file for the files (Using data from (SRP499796) sample,fastq_1,fastq_2,strandedness
- Fasta file of the trinity Contigs
- A GTF file
- A genebed file
- The tomato config file
Running this here: /projects/tomato_genome/fnb/dataprocessing/trinity/NEXTFLOW/hei-run1
Copied tomato config file from Molly's runs.
Got Fasts? Want GTF ? A perl script is hidden in the Trinity utils folder!! Works great.
perl /apps/pkg/trinity/2.14.0/util/misc/cdna_fasta_file_to_transcript_gtf.pl tamaulipas-trinity.Trinity.fasta | grep -w "exon" - > Trinity.gtf
After presenting a few of these results to Kevin, he suggested that we use tools other than Trinity for this process.
Specifically, the tools RNA-Spades and RNA BLOOM 2.
Going to end this task in favor of exploring these potentially better options.
New tasks will be made for them.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
This is a golden opportunity to test out Molly's pipeline document!
Used this document to run the pipeline: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit
And I will have Brandon try this out also and get familiar with the nextflow process.
This time however we will not be aligning to SL4 or SL5 but to the Trinity contigs.