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September 19, 2018 03:04
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ENCSR356KRQ_subsampled.json
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| ``` | |
| "atac.pipeline_type" : "atac", | |
| "atac.genome_tsv" : "/project2/name1/name2/DLDS/process_data/hg19db/hg19.tsv", | |
| "atac.fastqs" : [ | |
| [ | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz"], | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz"] | |
| ], | |
| [ | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz"], | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz"], | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz"], | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz"], | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz"], | |
| ["/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz", | |
| "/project2/name1/name2/DLDS/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz"] | |
| ] | |
| ], | |
| "atac.paired_end" : true, | |
| "atac.multimapping" : 4, | |
| "atac.trim_adapter.auto_detect_adapter" : true, | |
| "atac.trim_adapter.cpu" : 1, | |
| "atac.bowtie2.cpu" : 2, | |
| "atac.bowtie2.mem_mb" : 16000, | |
| "atac.filter.cpu" : 1, | |
| "atac.filter.mem_mb" : 12000, | |
| "atac.macs2_mem_mb" : 16000, | |
| "atac.smooth_win" : 73, | |
| "atac.enable_idr" : true, | |
| "atac.idr_thresh" : 0.05, | |
| "atac.qc_report.name" : "ENCSR356KRQ (subsampled 1/400 reads)", | |
| "atac.qc_report.desc" : "ATAC-seq on primary keratinocytes in day 0.0 of differentiation" | |
| } | |
| ``` |
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