Merging in changes from the pe2 cluster

[AdamStasiw]

The shared folder on the pe2 cluster contains a lot of work that hasn't been tracked in GitHub until now. This diff adds all of those changes, with the major caveat that it only includes scripts (.sh, .R, .Rmd, .py) and not any of the output or reference files (.txt, .tsv, .csv, .gtf, .log, etc.)

Specifically, here are the directories from pe2 that I ignored and did not include in this diff:

• 1.RawData_fastqs
• 2.Bam_files
• 3.Genotyping_info
• 4.Integrated_seurat_objs
• 5.Barcode_files
• 6.Junction_analysis_files (only kept scripts, not data - so 3.10x_juncs/primary_annotations, 1.Junction_calling_pipeline_ONT shell script and run_files R and Python scripts, and Alt5p_clusters Rmd)
• 7.Permutation_junction_output (only kept R_Notebooks directory)
• 8.Fisher_junction_output (only kept initial_processing/cryptic3p_analysis_preprocessing[.R | .sh])
• 9.Splice_pipeline_example_run (sample-specific data?)
• 10.Bam_splitting (only kept script files)
• 11.Alt3p_splicing_references (only kept .Rmd files)
• 12.Bulk.PSI (removed .tsv, .txt., .log, and .out files)
• 13.Motif.Analysis (removed log files and txt files)
• 14.APA.Analysis
• 15.Gene.Cards (only kept scripts)
• 16.Psuedotime.Window (only kept .R, .Rmd, and .sh files)
• 17.CH.MDS.Splice.Comparison (only kept .Rmd files)
• 18.A3SS.NMD.Expression (only kept .Rmd files)
• gmullokandov (user directory?)
• logs
• ONT_Splice_Pipeline (the existing github files were in this directory, with some modifications - I also removed the bin/gencode.v31.basic.annotation.gtf file, since it was over 100 Mb)
• NMD.caller (empty)
• squashed_fromONT
• unknown

[allyhawkins]

I would start with just the files from ONT_Splice_Pipeline as that is meant to be the meat of this and then work from there. A lot of the other folders are not related to the actual pipeline itself.

[AdamStasiw]

Makes sense! I put all of those other scripts into a new private repo: https://github.com/AdamStasiw/got_splice_analyses

I'll close this PR and make a fresh one with just that changes to this repo, now that I understand everything more clearly. Thanks!