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.

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

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

Moved files to:

/nobackup/tomato_genome/alt_splicing/for_igbquickload/junction_files

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

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.

[~aloraine]

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.