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15 July 2021, 06:34:57 UTC
Revision b165422254188ce4f89074374967f3390fd5d875 authored by emsanford on 25 February 2021, 23:34:09 UTC, committed by GitHub on 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
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Tip revision: b165422254188ce4f89074374967f3390fd5d875 authored by emsanford on 25 February 2021, 23:34:09 UTC
Update concat_zipped_fastq_files_from_illumina.py
Tip revision: b165422
README.md 
# atac-seq_pipeline_paired-end
Slightly customized version of the ENCODE ATAC-seq v1 pipeline. Made to run on Penn's high performance cluster (PMACS). The ENCODE ATAC-Seq pipeline v1 specifications are listed in this google doc: (specs at https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit#heading=h.9ecc41kilcvq

## Instructions for installing and running the pipeline are maintained at this google doc:
https://docs.google.com/document/d/1mpQp8NtI195oHWYb8pb_frV969209UIRCni3_gaWihw/edit

#### Additional info
This pipeline uses specific features of the PMACS high performance cluster at Penn. Some of the pipeline's reference files and required software are in a folder that is only available to Raj lab members. Please email me if you would like me a copy of these reference files.