Commits

Commits on Jan 24, 2024

Update README.md
aartrama
authoredJan 24, 2024

Commits on Jun 22, 2023

Adjust FPKM rule to allow exon,gene entries to differ in length
mestill7
authoredJun 22, 2023

Commits on Jun 5, 2023

Make table headers more clear
Aarthi
committedJun 5, 2023

Commits on Apr 26, 2023

Updated outdated config file; Improved multiqc template; Removed STAR alignment option
mestill7
committedApr 26, 2023

Commits on Mar 28, 2023

Repair syntax for duplicate removal
mestill7
authoredMar 28, 2023

Commits on Mar 27, 2023

Allow overlapping disconcordant reads in Cut&Run
mestill7
authoredMar 27, 2023

Commits on Mar 17, 2022

Instructions for using multiple cores on LSF added
aartrama
authoredMar 17, 2022

Commits on Mar 16, 2021

changed logs/ to output/logs/ for .o and .e files
aartrama
authoredMar 16, 2021

Commits on Aug 27, 2020

Revert STAR modifications intended for branch
mestill7
committedAug 27, 2020
STAR option added; Debug cut&run needed.
mestill7
committedAug 27, 2020

Commits on Aug 20, 2020

remove hidden files
aartrama
committedAug 20, 2020
clean up RNA-seq pipeline code
aartrama
committedAug 20, 2020

Commits on Aug 19, 2020

remove unwanted files
aartrama
committedAug 19, 2020
Revert "remove unwanted files"
aartrama
committedAug 19, 2020
remove unwanted files
aartrama
committedAug 19, 2020
gitignore updated
aartrama
committedAug 19, 2020
minor fixes
aartrama
committedAug 19, 2020

Commits on Jun 18, 2020

Single-end corrected and non-gzipped fastq files allowed
mestill7
committedJun 18, 2020

Commits on May 15, 2020

removed '_copy' from files
aartrama
authoredMay 15, 2020

Commits on Apr 27, 2020

Merge pull request #5 from mestill7/master
aartrama
authoredApr 27, 2020
Added cufflinks-compatible alignment option
mestill7
authoredApr 27, 2020
Add cufflinks option to config.yaml
mestill7
authoredApr 27, 2020

Commits on Mar 25, 2020

Update maximum sorting threads for Cut&Run
mestill7
authoredMar 25, 2020
Update Cut&Run documentation in README
mestill7
authoredMar 25, 2020

Commits on Mar 4, 2020

Update cluster.json for improved Cut&Run usage on large files
mestill7
committedMar 4, 2020
Improve Cut&Run read processing efficiency
mestill7
committedMar 4, 2020

Commits on Feb 6, 2020

Moved helper scriptto main directory
mestill7
committedFeb 6, 2020

Commits on Jan 29, 2020

Improved code formatting, added clarification regarding fastq filenames and modified Snakefile to remove redundant files generated during the snakemake run
mestill7
committedJan 29, 2020

Commits on Jan 10, 2020

Update .gitignore
lishen
committedJan 10, 2020

Commits on Jan 9, 2020

Update .gitignore
lishen
committedJan 9, 2020

Commits on Jan 4, 2020

Updated README
mestill7
committedJan 4, 2020
Simplified Snakefile structure and placed functions in external python file
mestill7
committedJan 4, 2020

Commits on Dec 2, 2019

Updated README file
mestill7
committedDec 2, 2019
Updated cluster.json walltimes and README file
mestill7
committedDec 2, 2019
Modified main Snakefile. Improved function structure and readability. Transferred code for trimming reads to sub-workflows.
mestill7
committedDec 2, 2019