Added scripts to new repository hotpollen/splicing-analysis.
Created new directory:

/nobackup/tomato_genome/alt_splicing/coverage_graph_bams

in UNCC cluster with symbolic links to bam files made in IGBF-3143 and IGBF-3163.

Made symbolic links to code in my home directory for generating coverage graphs. Launched jobs with:

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

Seems to be running OK.

Scripts used:

• src/sbatch-doIt.sh
• src/bamCoverage.sh

in repository https://bitbucket.org/hotpollen/splicing-analysis

Files are done.

I moved them to /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs.

To review:

• check that files have reasonable sizes (nothing non-zero)
• check that every ".scaled.bedgraph.gz" file has a corresponding ".scaled.bedgraph.gz.tbi" index file
• check that every "SRR" bam file in our control and experimental sample directories has a corresponding "scaled.bedgraph.gz" file

Review:

Directory- /nobackup/tomato_genome/alt_splicing/for_igbquickload/coverage_graphs

• No files seemed to have zero file size. Used command LL/ll.
• Every ".scaled.bedgraph.gz" file has a ".scaled.bedgraph.gz.tbi" file.
• Every "SRR" bam file in our control and experimental sample directories has a corresponding "scaled.bedgraph.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.