[IGBF-3507] Re-run Nextflow Muday time course data with SL4 and data downloaded from SRA - 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:
1
Epic Link:
Support NSF pollen grant
Sprint:
Fall 7, Spring 1, Spring 2, Spring 3, Spring 4

Description

SRP460750

Directory: /projects/tomato_genome/fnb/dataprocessing/SRP460750/

Only SL5 was rerun with the SRA data and SL4 needs to be run with data as well.

For this task, we need to confirm and sanity-check the muday time course data that Rob recently uploaded and submitted to the Sequence Read Archive.
If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
For this task:

Check SRP on NCBI and review submission
Download the data onto the cluster by using the SRP name
Run nf-core/rnaseq pipeline
Run our coverage graph and junctions scripts on the data

Note that all files should now use their "SRR" names instead of the existing file names.

Attachments

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Attachments

muday-144-SL4-multiqc_report.html
5.95 MB
19/Feb/24 3:40 PM
muday-144-SL5-multiqc_report.html
5.92 MB
19/Feb/24 3:40 PM

Issue Links

relates to

IGBF-3627 Create sample sheet for SRP460750

Closed

IGBF-3720 Re-run Nextflow Muday time course data again with SL5 and data downloaded from SRA

Closed

IGBF-3406 Re-run Nextflow Muday time course data with SL5 data downloaded from SRA

Closed

Activity

Ascending order - Click to sort in descending order

Molly Davis created issue - 07/Dec/23 10:10 AM

Molly Davis made changes - 07/Dec/23 10:10 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Molly Davis made changes - 07/Dec/23 10:10 AM

Link

This issue relates to ~~IGBF-3406~~ [ ~~IGBF-3406~~ ]

Molly Davis made changes - 07/Dec/23 10:43 AM

Sprint

Fall 7 [ 183 ]

Molly Davis made changes - 07/Dec/23 4:38 PM

Description

SRP460750

*Directory*: /projects/tomato_genome/fnb/dataprocessing/SRP460750/

Only SL5 was rerun with the SRA data and SL4 needs to be run with data as well.

SRP460750

*Directory*: /projects/tomato_genome/fnb/dataprocessing/SRP460750/

Only SL5 was rerun with the SRA data and SL4 needs to be run with data as well.

For this task, we need to confirm and sanity-check the muday time course data that Rob recently uploaded and submitted to the Sequence Read Archive.
If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
For this task:
* Check SRP on NCBI and review submission
* Download the data onto the cluster by using the SRP name
* Run nf-core/rnaseq pipeline
* Run our coverage graph and junctions scripts on the data

Note that all files should now use their "SRR" names instead of the existing file names.

Molly Davis made changes - 07/Dec/23 4:49 PM

Sprint

Fall 7 [ 183 ]

Molly Davis made changes - 07/Dec/23 4:50 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 11/Dec/23 9:44 AM

Sprint

Fall 7 [ 183 ]

Fall 7, Fall 8 [ 183, 184 ]

Ann Loraine made changes - 11/Dec/23 9:44 AM

Rank

Ranked higher

Molly Davis made changes - 11/Dec/23 10:51 AM

Comment

[ *Re-run Directory*: /projects/tomato_genome/fnb/dataprocessing/SRP460750

*Prefetch SRR Script*:

{code:java}

#! /bin/bash

#SBATCH --job-name=prefetch_SRR
#SBATCH --partition=Orion
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=4gb
#SBATCH --output=%x_%j.out
#SBATCH --time=24:00:00

cd /projects/tomato_genome/fnb/dataprocessing/SRP460750
module load sra-tools/2.11.0
vdb-config --interactive

files=(
SRR25478240
SRR25478241
SRR25478242
SRR25478243
SRR25478244
SRR25478245
SRR25478246
SRR25478247
SRR25478248
SRR25478249
SRR25478250
SRR25478251
SRR25478252
SRR25478253
SRR25478254
SRR25478255
SRR25478256
SRR25478257
SRR25478258
SRR25478259
SRR25478260
SRR25478261
SRR25478262
SRR25478263
SRR25478264
SRR25478265
SRR25478266
SRR25478267
SRR25478268
SRR25478269
SRR25478270
SRR25478271
SRR25478272
SRR25478273
SRR25478274
SRR25478275
SRR25478276
SRR25478277
SRR25478278
SRR25478279
SRR25478280
SRR25478281
SRR25478282
SRR25478283
SRR25478284
SRR25478285
SRR25478286
SRR25478287
SRR25478288
SRR25478289
SRR25478290
SRR25478291
SRR25478292
SRR25478293
SRR25478294
SRR25478295
SRR25478296
SRR25478297
SRR25478298
SRR25478299
SRR25478300
SRR25478301
SRR25478302
SRR25478303
SRR25478304
SRR25478305
SRR25478306
SRR25478307
SRR25478308
SRR25478309
SRR25478310
SRR25478311

)

for f in "${files[@]}"; do echo $f; prefetch $f; done

{code}

*Execute*:

{code:java}
chmod u+x prefetch.slurm
{code}

{code:java}
sbatch prefetch.slurm
{code}

*Faster Dump Script*:

{code:java}
#! /bin/bash

#SBATCH --job-name=fastqdump_SRR
#SBATCH --partition=Orion
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=40gb
#SBATCH --output=%x_%j.out
#SBATCH --time=24:00:00
#SBATCH --array=1-72

#setting up where to grab files from
file=$(sed -n -e "${SLURM_ARRAY_TASK_ID}p" /projects/tomato_genome/fnb/dataprocessing/SRP460750/Sra_ids.txt)

cd /projects/tomato_genome/fnb/dataprocessing/SRP460750
module load sra-tools/2.11.0

echo "Starting faster-qdump on $file";

cd /projects/tomato_genome/fnb/dataprocessing/SRP460750/$file

fasterq-dump ${file}.sra

perl /projects/tomato_genome/scripts/validateHiseqPairs.pl ${file}_1.fastq ${file}_2.fastq

cp ${file}_1.fastq /projects/tomato_genome/fnb/dataprocessing/SRP460750/${file}_1.fastq
cp ${file}_2.fastq /projects/tomato_genome/fnb/dataprocessing/SRP460750/${file}_2.fastq

echo "finished"
{code}

*Execute*:

{code:java}
chmod u+x fasterdump.slurm
{code}

{code:java}
sbatch fasterdump.slurm
{code}
]

Molly Davis made changes - 15/Dec/23 2:20 PM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 22/Dec/23 10:24 AM

Sprint

Fall 7, Fall 8 [ 183, 184 ]

Fall 7, Spring 2 [ 183, 186 ]

Molly Davis made changes - 16/Jan/24 9:50 AM

Sprint

Fall 7, Spring 2 [ 183, 186 ]

Fall 7, Spring 1 [ 183, 185 ]

Molly Davis made changes - 16/Jan/24 10:46 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Molly Davis made changes - 17/Jan/24 10:00 AM

Assignee

Molly Davis [ molly ]

Molly Davis made changes - 17/Jan/24 10:00 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Molly Davis made changes - 17/Jan/24 10:00 AM

Assignee

Robert Reid [ robertreid ]

Ann Loraine made changes - 20/Jan/24 4:45 PM

Sprint

Fall 7, Spring 1 [ 183, 185 ]

Fall 7, Spring 1, Spring 2 [ 183, 185, 186 ]

Ann Loraine made changes - 20/Jan/24 4:45 PM

Rank

Ranked higher

Robert Reid made changes - 25/Jan/24 12:03 PM

Assignee

Robert Reid [ robertreid ]

Molly Davis [ molly ]

Robert Reid made changes - 25/Jan/24 12:04 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Molly Davis made changes - 25/Jan/24 3:49 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Molly Davis made changes - 26/Jan/24 9:50 AM

Rank

Ranked higher

Molly Davis made changes - 26/Jan/24 3:44 PM

Assignee

Molly Davis [ molly ]

Molly Davis made changes - 26/Jan/24 3:44 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Molly Davis made changes - 26/Jan/24 3:44 PM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 02/Feb/24 6:27 PM

Sprint

Fall 7, Spring 1, Spring 2 [ 183, 185, 186 ]

Fall 7, Spring 1, Spring 2, Spring 3 [ 183, 185, 186, 187 ]

Ann Loraine made changes - 02/Feb/24 6:27 PM

Rank

Ranked higher

Ann Loraine made changes - 16/Feb/24 10:10 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 16/Feb/24 10:10 AM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 16/Feb/24 10:11 AM

Assignee

Ann Loraine [ aloraine ]

Molly Davis made changes - 16/Feb/24 2:26 PM

Assignee

Molly Davis [ molly ]

Ann Loraine made changes - 19/Feb/24 9:21 AM

Sprint

Fall 7, Spring 1, Spring 2, Spring 3 [ 183, 185, 186, 187 ]

Fall 7, Spring 1, Spring 2, Spring 3, Spring 4 [ 183, 185, 186, 187, 188 ]

Ann Loraine made changes - 19/Feb/24 9:21 AM

Rank

Ranked higher

Molly Davis made changes - 19/Feb/24 3:40 PM

Attachment		muday-144-SL4-multiqc_report.html [ 18224 ]
Attachment		muday-144-SL5-multiqc_report.html [ 18225 ]

Molly Davis made changes - 19/Feb/24 3:48 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Molly Davis made changes - 19/Feb/24 3:48 PM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Molly Davis made changes - 28/Feb/24 4:49 PM

Link

This issue relates to ~~IGBF-3627~~ [ ~~IGBF-3627~~ ]

Molly Davis made changes - 07/May/24 10:26 AM

Link

This issue relates to ~~IGBF-3720~~ [ ~~IGBF-3720~~ ]

People

Assignee:

Molly Davis

Reporter:

Molly Davis

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

07/Dec/23 10:10 AM

Updated:

07/May/24 10:26 AM

Resolved:

19/Feb/24 3:48 PM