https://github.com/arjunrajlaboratory/atac-seq_pipeline_paired-end

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Revision Author Date Message Commit Date
c4c819e Create LICENSE 17 December 2020, 01:16:43 UTC
cb04e17 minor documentation update 23 January 2020, 15:54:23 UTC
96e21d2 updated readme 23 January 2020, 15:17:11 UTC
2063f84 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 Create README.md 23 January 2020, 15:09:44 UTC
fbdada8 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 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 edited grep command to remove non-full chromosomes from macs2 output files 04 April 2019, 18:39:24 UTC
ea74736 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 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 progress update; most of code refactoring complete 05 September 2018, 16:42:33 UTC
c347071 final commit before refactoring code into more functional and object-oriented style 04 September 2018, 16:28:23 UTC
3b70772 added peak calling with MACS2 24 July 2018, 21:18:32 UTC
fd3a437 removed multimapping feature from bowtie2; had no intention of using secondary alignments 18 July 2018, 20:36:32 UTC
d8df4bd Updating plumbing to allow for batch job submissions, using the submit_batch_atac_pipelines.py file. 18 July 2018, 19:08:40 UTC
1872389 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 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 added tagAlign file, bedpe file, and subsample file creation (subsample file untested at this point) 22 June 2018, 21:07:55 UTC
f130c7b 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 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 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
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