[IGBF-3043] Align and process rice RNA-Seq data using nf-core/rnaseq pipeline - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Publish rice splicing and methylation results
Sprint:
Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11

Description

Align and process RNA-Seq data using nf-core/rnaseq pipeline

Attachments

Issue Links

relates to

IGBF-3099 Analyze differential expression using RNA-Seq

To-Do

Activity

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Ann Loraine created issue - 23/Dec/21 7:11 AM

Ann Loraine made changes - 23/Dec/21 7:11 AM

Field	Original Value	New Value
Epic Link		IGBF-3039 [ 21553 ]

Ann Loraine made changes - 17/Jan/22 11:09 PM

Sprint

Spring 1 2022 Jan 3 - Jan 14 [ 136 ]

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ]

Ann Loraine made changes - 17/Jan/22 11:09 PM

Rank

Ranked higher

Ann Loraine made changes - 24/Jan/22 12:18 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 24/Jan/22 12:18 PM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 24/Jan/22 5:33 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 25/Jan/22 9:17 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 25/Jan/22 9:51 AM

Comment

[ More errors:

{code}
  >>>>> Now validing the length of the 2 paired-end infiles: A.C.Y.S.3_1_trimmed.fq.gz and A.C.Y.S.3_2_trimmed.fq.gz <<<<<
  Writing validated paired-end Read 1 reads to A.C.Y.S.3_1_val_1.fq.gz
  Writing validated paired-end Read 2 reads to A.C.Y.S.3_2_val_2.fq.gz

  Read 2 output is truncated at sequence count: 23469680, please check your paired-end input files! Terminating...

  INFO: Cleaning up image...

Work dir:
  /nobackup/lorainelab/salty_rice/rna-seq/work/c7/25844b7fa5600e4c60222407461493

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
{code}

]

Ann Loraine made changes - 25/Jan/22 10:34 AM

Description

Align and process RNA-Seq data using nf-core/rnaseq pipeline

Ann Loraine made changes - 26/Jan/22 10:25 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 26/Jan/22 10:25 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 27/Jan/22 7:47 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 29/Jan/22 11:22 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 29/Jan/22 12:32 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 30/Jan/22 1:22 PM

Sprint

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ]

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 136, 137, 138 ]

Ann Loraine made changes - 30/Jan/22 1:22 PM

Rank

Ranked higher

Ann Loraine made changes - 30/Jan/22 1:23 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 31/Jan/22 10:17 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 13/Feb/22 6:17 PM

Sprint

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11 [ 136, 137, 138 ]

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 136, 137, 138, 139 ]

Ann Loraine made changes - 13/Feb/22 6:17 PM

Rank

Ranked higher

Ann Loraine made changes - 22/Feb/22 9:46 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 22/Feb/22 12:07 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 24/Feb/22 11:52 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 25/Feb/22 10:05 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 25/Feb/22 10:05 AM

Assignee

Ann Loraine [ aloraine ]

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 25/Feb/22 2:38 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 25/Feb/22 3:38 PM

Assignee

Nowlan Freese [ nfreese ]

Ann Loraine [ aloraine ]

Nowlan Freese made changes - 25/Feb/22 3:38 PM

Status

First Level Review in Progress [ 10301 ]

To-Do [ 10305 ]

Ann Loraine made changes - 26/Feb/22 1:28 PM

Sprint

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25 [ 136, 137, 138, 139 ]

Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28, Spring 3 2022 Jan 31 - Feb 11, Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11 [ 136, 137, 138, 139, 140 ]

Ann Loraine made changes - 26/Feb/22 1:28 PM

Rank

Ranked higher

Ann Loraine made changes - 03/Mar/22 8:19 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 03/Mar/22 8:19 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 03/Mar/22 10:30 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 03/Mar/22 2:17 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 03/Mar/22 2:17 PM

Assignee

Ann Loraine [ aloraine ]

Nowlan Freese made changes - 07/Mar/22 9:27 AM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 07/Mar/22 9:27 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 07/Mar/22 10:02 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 07/Mar/22 10:02 AM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]