[IGBF-3165] Make junction files for experimental and positive control alignments data - 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:
Support NSF pollen grant
Sprint:
Fall 1 2022 Aug 15, Fall 2 2022 Sep 5

Description

Run the "find junctions" program to generate spreadsheets showing support for splicing events.

This program generates bed format files that tabulate evidence supporting splicing. The "score" field of the output file indicates the number sequence alignments that exhibit evidence of splicing in a particular location, called a "junction".

This format for representing splicing events comes originally from the "tophat" program, which generates "bed" files containing junctions in essentially the same way.

Attachments

Issue Links

blocks

IGBF-3172 Tabulate splicing support by running arabitag algorithm on junction and bam files

Closed

is blocked by

IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

Closed

Activity

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Ann Loraine created issue - 31/Aug/22 4:26 PM

Ann Loraine made changes - 31/Aug/22 4:26 PM

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

Ann Loraine made changes - 31/Aug/22 4:26 PM

Link

This issue is blocked by ~~IGBF-3143~~ [ ~~IGBF-3143~~ ]

Ann Loraine made changes - 31/Aug/22 4:26 PM

Rank

Ranked higher

Ann Loraine made changes - 31/Aug/22 4:46 PM

Summary

Generate junction files for experimental and positive control alignments data

Make junction files for experimental and positive control alignments data

Ann Loraine made changes - 02/Sep/22 12:59 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Ann Loraine made changes - 02/Sep/22 6:47 PM

Sprint

Fall 1 2022 Aug 15 [ 153 ]

Fall 1 2022 Aug 15, Fall 2 2022 Sep 5 [ 153, 154 ]

Ann Loraine made changes - 02/Sep/22 6:48 PM

Rank

Ranked higher

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Ann Loraine added a comment - 07/Sep/22 12:29 PM - edited

Added new files to hotpollen/splicing_analysis repository:

find_junctions.sh
sbatch-doIt.sh
find-junctions "jar" file

Checked that the system has java:

[aloraine@str-i1 bams]$ java -version
openjdk version "1.8.0_342"
OpenJDK Runtime Environment (build 1.8.0_342-b07)
OpenJDK 64-Bit Server VM (build 25.342-b07, mixed mode)

Created new directory "bams" with symbolic links to all the BAM files and their indexes made in ~~IGBF-3143~~.
Made symbolic links to above scripts and jar file within this location.
Launched jobs with:

sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err

Got error:

Error: Invalid or corrupt jarfile find-junctions-1.0.0-jar-with-dependencies.jar

Fixed it by copying a fresher version of the jar file to the "src" directory in my home folder.

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Ann Loraine added a comment - 07/Sep/22 12:29 PM - edited Added new files to hotpollen/splicing_analysis repository: find_junctions.sh sbatch-doIt.sh find-junctions "jar" file Checked that the system has java: [aloraine@str-i1 bams]$ java -version openjdk version "1.8.0_342" OpenJDK Runtime Environment (build 1.8.0_342-b07) OpenJDK 64-Bit Server VM (build 25.342-b07, mixed mode) Created new directory "bams" with symbolic links to all the BAM files and their indexes made in IGBF-3143 . Made symbolic links to above scripts and jar file within this location. Launched jobs with: sbatch-doIt.sh .bam find_junctions.sh >jobs.out 2>jobs.err Got error: Error: Invalid or corrupt jarfile find-junctions-1.0.0-jar-with-dependencies.jar Fixed it by copying a fresher version of the jar file to the "src" directory in my home folder.

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Ann Loraine added a comment - 07/Sep/22 12:48 PM

Forgot to include the 2bit file in the directory. Adding it and restarting the jobs.

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Ann Loraine added a comment - 07/Sep/22 12:48 PM Forgot to include the 2bit file in the directory. Adding it and restarting the jobs.

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Ann Loraine added a comment - 07/Sep/22 1:24 PM

Jobs look done, with 66 ".tbi" index files, one per each of the 66 input .bam files.

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Ann Loraine added a comment - 07/Sep/22 1:24 PM Jobs look done, with 66 ".tbi" index files, one per each of the 66 input .bam files.

Ann Loraine made changes - 07/Sep/22 1:26 PM

Link

This issue blocks ~~IGBF-3172~~ [ ~~IGBF-3172~~ ]

Ann Loraine made changes - 07/Sep/22 1:40 PM

Description

Run the "find junctions" program to generate spreadsheets showing support for splicing events.

Ann Loraine made changes - 07/Sep/22 1:41 PM

Description

Run the "find junctions" program to generate spreadsheets showing support for splicing events.

This program generates bed format files that tabulate evidence supporting splicing. The "score" field of the output file indicates the number sequence alignments that exhibit evidence of splicing in a particular location, called a "junction".

This format for representing splicing events comes originally from the "tophat" program, which generates "bed" files containing junctions in essentially the same way.

Ann Loraine made changes - 08/Sep/22 11:38 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Ann Loraine made changes - 08/Sep/22 3:19 PM

Assignee

Ann Loraine [ aloraine ]

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Ann Loraine added a comment - 08/Sep/22 3:20 PM

Moved files to:

/nobackup/tomato_genome/alt_splicing/for_igbquickload/junction_files

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Ann Loraine added a comment - 08/Sep/22 3:20 PM Moved files to: /nobackup/tomato_genome/alt_splicing/for_igbquickload/junction_files

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Ann Loraine added a comment - 08/Sep/22 3:21 PM - edited

To review:

check that files have reasonable sizes (no "zero" size files, for example)
check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
check that every "SRR" bam file in our control and experimental sample directories has a corresponding "FJ.bed.gz" file

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Ann Loraine added a comment - 08/Sep/22 3:21 PM - edited To review: check that files have reasonable sizes (no "zero" size files, for example) check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file check that every "SRR" bam file in our control and experimental sample directories has a corresponding "FJ.bed.gz" file

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Molly Davis (Inactive) added a comment - 14/Sep/22 10:54 AM

Review:

Directory- /nobackup/tomato_genome/alt_splicing/for_igbquickload/junction_files

No files were zero size. Used command LL/ll.
Every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
Every "SRR" bam file in our control and experimental sample directories has a corresponding "FJ.bed.gz" file. SRP328042-molly SRR files are in-between SRP252265 files in the directory might be hard to differentiate which is control and which is experimental.

Ann Loraine

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Molly Davis (Inactive) added a comment - 14/Sep/22 10:54 AM Review: Directory- /nobackup/tomato_genome/alt_splicing/for_igbquickload/junction_files No files were zero size. Used command LL/ll. Every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file Every "SRR" bam file in our control and experimental sample directories has a corresponding "FJ.bed.gz" file. SRP328042-molly SRR files are in-between SRP252265 files in the directory might be hard to differentiate which is control and which is experimental. Ann Loraine

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Ann Loraine added a comment - 18/Sep/22 9:12 AM

Thanks [~molly]. I decided to store all the files in the same folder and will use an index / table of contents type strategy to distinguish them. Moving to Done.

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Ann Loraine added a comment - 18/Sep/22 9:12 AM Thanks [~molly] . I decided to store all the files in the same folder and will use an index / table of contents type strategy to distinguish them. Moving to Done.