Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Minor
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:4
-
Epic Link:
-
Sprint:Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7, Fall 1
Description
GOAL:
To set up and run an nf-core/rna-seq pipeline to align our RNA-Seq sequences against the de novo created contigs (Trinity, Spades).
Next flow requires a GTF and a bed file along with the contigs. There are various ways to generate these and it is possible issues will arise from these files.
Otherwise, we can follow Molly's protocol:
https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit?usp=sharing
Attachments
Issue Links
- blocks
-
-
- To-Do
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 2 [ 196 ] | Summer 2, Summer 3 [ 196, 197 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Sprint | Summer 2, Summer 3 [ 196, 197 ] | Summer 2, Summer 3, Summer 4 [ 196, 197, 198 ] |
| Rank | Ranked higher |
| Description |
GOAL:
To set up and run nextflow on our various de novo created contigs (Trinity, Spades). Next flow requires a GTF and a bed file along with the contigs. There are various ways to generate these and it is possible issues will arise from these files. Otherwise, we can follow Molly's protocol: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit?usp=sharing |
GOAL:
To set up and run an nf-core/rna-seq pipeline to align our RNA-Seq sequences against the de novo created contigs (Trinity, Spades). Next flow requires a GTF and a bed file along with the contigs. There are various ways to generate these and it is possible issues will arise from these files. Otherwise, we can follow Molly's protocol: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit?usp=sharing |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Sprint | Summer 2, Summer 3, Summer 4 [ 196, 197, 198 ] | Summer 2, Summer 3, Summer 4, Summer 5 [ 196, 197, 198, 199 ] |
| Rank | Ranked higher |
| Comment |
[ Besthits.fna file had many duplicates causing errors with the samtools sort command, resulting in the pipeline dying on me. I made a tmp directory so I could troubleshoot. I removed all duplicates using this command: awk '!seen[$1]++' heinz_rna_spades.gtf > heinz_bestlonghit_no_dupes.fna. Nextflow was completed successfully after using the no dupes file as my fasta file.
Results: /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/Hei-run-1/tmp ] |
| Sprint | Summer 2, Summer 3, Summer 4, Summer 5 [ 196, 197, 198, 199 ] | Summer 2, Summer 3, Summer 4, Summer 5, Summer 6 [ 196, 197, 198, 199, 200 ] |
| Rank | Ranked higher |
| Sprint | Summer 2, Summer 3, Summer 4, Summer 5, Summer 6 [ 196, 197, 198, 199, 200 ] | Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7 [ 196, 197, 198, 199, 200, 201 ] |
| Rank | Ranked higher |
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
| Assignee | Robert Reid [ robertreid ] | Brandon Bendickson [ bbendick ] |
| Story Points | 3 | 4 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Rank | Ranked lower |
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
| Sprint | Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7 [ 196, 197, 198, 199, 200, 201 ] | Summer 2, Summer 3, Summer 4, Summer 5, Summer 6, Summer 7, Fall 1 [ 196, 197, 198, 199, 200, 201, 202 ] |
| Rank | Ranked higher |
| 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 ] |