| b165422 | emsanford | 25 February 2021, 23:34:09 UTC | Update concat_zipped_fastq_files_from_illumina.py Do not include replicate number in the sample key by default | 25 February 2021, 23:34:09 UTC |
| c4c819e | emsanford | 17 December 2020, 01:16:43 UTC | Create LICENSE | 17 December 2020, 01:16:43 UTC |
| cb04e17 | Eric Sanford | 23 January 2020, 15:54:23 UTC | minor documentation update | 23 January 2020, 15:54:23 UTC |
| 96e21d2 | Eric Sanford | 23 January 2020, 15:17:11 UTC | updated readme | 23 January 2020, 15:17:11 UTC |
| 2063f84 | Eric Sanford | 23 January 2020, 15:15:25 UTC | fixed typo in set_atac_pmacs_env that would prevent unloading the picard/1.96 module after using it. did not cause any known issues. | 23 January 2020, 15:15:25 UTC |
| 21bcd44 | emsanford | 23 January 2020, 15:09:44 UTC | Create README.md | 23 January 2020, 15:09:44 UTC |
| fbdada8 | Eric Sanford | 23 September 2019, 20:55:26 UTC | Changed default MACS2 parameter from p=0.01 to q=0.05. updated concat_zipped_fastq files script to take in command line files instead of requiring editing of the script. | 23 September 2019, 20:55:26 UTC |
| c9d62f7 | Eric Sanford | 23 July 2019, 14:22:16 UTC | Moved reference files to shared location on /project/arjunrajlab/<resources||refs>, increased memory limit for batch jobs, added exception handling and error messages for improperly named fastq input files, and relaxed permissions for all files. | 23 July 2019, 14:22:16 UTC |
| 45c7c8f | Eric Sanford | 04 April 2019, 18:39:24 UTC | edited grep command to remove non-full chromosomes from macs2 output files | 04 April 2019, 18:39:24 UTC |
| ea74736 | Eric Sanford | 03 April 2019, 22:37:42 UTC | Created new MACS2 output files, with removed chrUnXX non-full chromosome entries. Also added new blacklist-filtered files that do not max out at 300k peaks | 03 April 2019, 22:37:42 UTC |
| 50e2c96 | Eric Sanford | 15 October 2018, 21:25:41 UTC | Minor modifications to ATAC pipeline to accomodate HDD1 experiment sample name patterns. Added script to collect post-sequencing metrics | 15 October 2018, 21:25:41 UTC |
| 371fc50 | Eric Sanford | 05 September 2018, 16:42:33 UTC | progress update; most of code refactoring complete | 05 September 2018, 16:42:33 UTC |
| c347071 | Eric Sanford | 04 September 2018, 16:28:23 UTC | final commit before refactoring code into more functional and object-oriented style | 04 September 2018, 16:28:23 UTC |
| 3b70772 | Eric Sanford | 24 July 2018, 21:18:32 UTC | added peak calling with MACS2 | 24 July 2018, 21:18:32 UTC |
| fd3a437 | Eric Sanford | 18 July 2018, 20:36:32 UTC | removed multimapping feature from bowtie2; had no intention of using secondary alignments | 18 July 2018, 20:36:32 UTC |
| d8df4bd | Eric Sanford | 18 July 2018, 19:08:40 UTC | Updating plumbing to allow for batch job submissions, using the submit_batch_atac_pipelines.py file. | 18 July 2018, 19:08:40 UTC |
| 1872389 | Eric Sanford | 29 June 2018, 21:38:21 UTC | Pipeline development switched to the cluster. This commit successfully runs on an interactive node on the cluster, from read alignment to read filtered to some QC file generation and read downsampling. | 29 June 2018, 21:38:21 UTC |
| 02203a9 | Eric Sanford | 26 June 2018, 22:01:26 UTC | added set_atac_pmacs_env file as a wrapper command for running the pipeline on the Penn PMACS cluster. future commits will be geared towards running the pipeline on PMACS | 26 June 2018, 22:01:26 UTC |
| 4adfae9 | Eric Sanford | 22 June 2018, 21:07:55 UTC | added tagAlign file, bedpe file, and subsample file creation (subsample file untested at this point) | 22 June 2018, 21:07:55 UTC |
| f130c7b | Eric Sanford | 22 June 2018, 18:01:58 UTC | added mapping quality filter, requiring map quality of at least 20. A larger portion of the reads kept after removing the assign_multimappers script had low map qualities. Using the map quality filter results in higher coverage and likely higher quality data. | 22 June 2018, 18:01:58 UTC |
| f78cee4 | Eric Sanford | 21 June 2018, 20:33:41 UTC | removed the assign_multimappers.py script from the pipeline. I found that it does not actually assign multimapped reads and it ends up discarding reads that have as many candidate alignments as defined by the -k parameter. | 21 June 2018, 20:33:41 UTC |
| dd27f86 | Eric | 21 June 2018, 16:45:22 UTC | initial commit. first step of pipeline, aligning and filtering reads, is working on a test paired-end read example. | 21 June 2018, 16:45:22 UTC |
