This pipeline is largely based on Encode pipeline, with few small changes.:
fastq.bz files More detailed documentation can be found on this gitbook.
== atac pipeline settings
-type <string> : Type of the pipeline. atac-seq or chip-seq (default: atac-seq).
-chip_seq <bool> : Chip-Seq (no tn5 shifting).
-trimmed_fastq <bool> : Skip fastq-trimming stage.
-align <bool> : Align only (no MACS2 peak calling or IDR or ataqc analysis).
-subsample_xcor <string> : # reads to subsample for cross corr. analysis (default: 25M).
-subsample <string> : # reads to subsample exp. replicates. Subsampled tagalign will be used for steps downstream (default: 0; no subsampling).
-true_rep <bool> : No pseudo-replicates.
-no_ataqc <bool> : No ATAQC
-no_xcor <bool> : No Cross-correlation analysis.
-csem <bool> : Use CSEM for alignment.
-smooth_win <string> : Smoothing window size for MACS2 peak calling (default: 150).
-idr_thresh <real> : IDR threshold : -log_10(score) (default: 0.1).
-old_trimmer <bool> : Use legacy trim adapters (trim_galore and trimAdapter.py).
-ENCODE3 <bool> : Force to use parameter set (-smooth_win 73 -idr_thresh 0.05 -multimapping 4) for ENCODE3.
-ENCODE <bool> : Force to use parameter set (-smooth_win 73 -idr_thresh 0.05 -multimapping 4) for ENCODE.
-no_browser_tracks <bool> : Disable generation of genome browser tracks (workaround for bzip2 shared library issue).
-overlap_pval_thresh <real> : p-val threshold for overlapped peaks (default: 0.01).
-macs2_pval_thresh <real> : MACS2 p-val threshold for calling peaks (default: 0.1).
-macs2_pval_thresh_bw <real> : MACS2 p-val threshold for generating BIGWIG signal tracks (default: 0.1).
-enable_idr <bool> : Enable IDR on called peaks.
== configuration file settings
-c <string> : Configuration file path.
-env <string> : Environment file path.
== parallelization settings
-no_par <bool> : Serialize all tasks (individual tasks can still use multiple threads up to '-nth').
-nth <int> : Maximum # threads for a pipeline. (default: 8).
== cluster/system/resource settings
-wt <string> : Walltime for all single-threaded tasks (example: 8:10:00, 3h, 3600, default: 5h50m, 5:50:00).
-memory <string> : Maximum memory for all single-threaded tasks (equivalent to '-mem', example: 4.5G, 1024M, default: 7G).
-use_system <string> : Force to use a system (equivalent to 'bds -s [SYSTEM_NAME] ...', any system defined in bds.config can be used).
-nice <int> : Set process priority for all tasks (default: 0; -20 (highest) ~ 19 (lowest) ).
-retrial <int> : # of Retrial for failed tasks (default: 0).
-q <string> : Submit tasks to a specified cluster queue.
-unlimited_mem_wt <bool> : Use unlimited max. memory and walltime.
== shell environment settings
-mod <string> : Modules separated by ; (example: "bowtie/2.2.4; bwa/0.7.7; picard-tools/1.92").
-shcmd <string> : Shell commands separated by ;. Shell var. must be written as ${VAR} not as $VAR (example: "export PATH=${PATH}:/usr/test; VAR=test").
-addpath <string> : Path separated by ; or : to be PREPENDED to \$PATH (example: "/bin/test:${HOME}/utils").
-conda_env <string> : Anaconda Python (or Miniconda) environment name for all softwares including Python2.
-conda_env_py3 <string> : Anaconda Python (or Miniconda) environment name for Python3.
-conda_bin_dir <string> : Anaconda Python (or Miniconda) bin directory.
-cluster_task_min_len <int> : Minimum length for a cluster job in seconds (dealing with NFS delayed write, default: 60).
-cluster_task_delay <int> : Constant delay for every job in seconds (dealing with NFS delayed write, default: 0).
== output/title settings
-out_dir <string> : Output directory (default: out).
-title <string> : Prefix for HTML report and outputs without given prefix.
== species settings
-species <string> : Species. need to specify '-species_file' too if you have not installed genome database with 'install_genome_data.sh'.
-species_file <string> : Species file path.
-species_browser <string> : Species name in WashU genome browser.
-ref_fa <string> : Reference genome sequence fasta.
-chrsz <string> : Chromosome sizes file path (use fetchChromSizes from UCSC tools).
-blacklist <string> : Blacklist bed.
-seq_dir <string> : Reference genome sequence directory path (where chr*.fa exist).
== ENCODE accession settings
-ENCODE_accession <string> : ENCODE experiment accession ID (or dataset).
-ENCODE_award_rfa <string> : ENCODE award RFA (e.g. ENCODE3).
-ENCODE_assay_category <string> : ENCODE assay category.
-ENCODE_assay_title <string> : ENCODE assay title.
-ENCODE_award <string> : ENCODE award (e.g. /awards/U41HG007000/).
-ENCODE_lab <string> : Lab (e.g. /labs/anshul-kundaje/)
-ENCODE_assembly <string> : hg19, GRCh38, mm9, mm10.
-ENCODE_alias_prefix <string> : Alias prefix, Alias = alias_prefix: + filename + alias_suffix
-ENCODE_alias_suffix <string> : Alias suffix, Alias = alias_prefix: + filename + alias_suffix
== report settings
-url_base <string> : URL base for output directory.
-viz_genome_coord <string> : WashU genome browser genome coordinate (e.g. chr7:27117661-27153380).
== fastq input definition :
Single-ended : For replicate '-fastq[REP_ID]', For control '-ctl_fastq[REP_ID]'
Paired end : For replicate '-fastq[REP_ID]_[PAIR_ID]', For control '-ctl_fastq[REP_ID]_[PAIR_ID]'
== bam input (raw or filtered) definition :
Raw bam : For replicate '-bam[REP_ID]', For control '-ctl_bam[REP_ID]'.
Filtered bam : For replicate '-filt_bam[REP_ID]', For control '-ctl_filt_bam[REP_ID]'.
== tagalign input definition :
For replicate '-tag[REP_ID]', For control '-ctl_tag[REP_ID]'.
== narrow peak input definition :
For true replicates, use '-peak1' and '-peak2',
For pooled replicates, use '-peak_pooled',
For two PR (self-pseudo-replicates), use '-peak[REP_ID]_pr1' and '-peak[REP_ID]_pr2'
For two PPR (pooled pseudo-replicates), use '-peak_ppr1' and '-peak_ppr2'
== input endedness settings (SE or PE) :
-se <bool> : Singled-ended data set. To specify it for each replicate, '-se[REP_ID]' for exp. reps, '-ctl_se[CTL_ID]' for control.
-pe <bool> : Paired end data set. To specify it for each replicate, '-pe[REP_ID]' for exp. reps, '-ctl_pe[CTL_ID]' for controls.
== adapter sequence definition :
Single-ended : For replicate '-adapter[REP_ID]'
Paired end : For replicate '-adapter[REP_ID]_[PAIR_ID]'
== align multimapping settings
-multimapping <int> : # alignments reported for multimapping (default: 0).
== align bowtie2 settings (requirements: -bwt2_idx)
-bwt2_idx <string> : Bowtie2 index (full path prefix of *.1.bt2 file).
-scoremin_bwt2 <string> : Replacement --score-min for bowtie2.
-wt_bwt2 <string> : Walltime for bowtie2 (default: 47h, 47:00:00).
-mem_bwt2 <string> : Max. memory for bowtie2 (default: 12G).
-extra_param_bwt2 <string> : Extra parameter for bowtie2.
== adapter trimmer settings
-adapter_err_rate <string> : Maximum allowed adapter error rate (# errors divided by the length of the matching adapter region, default: 0.10).
-min_trim_len <int> : Minimum trim length for cutadapt -m, throwing away processed reads shorter than this (default: 5).
-wt_trim <string> : Walltime for adapter trimming (default: 23h, 23:00:00).
-mem_trim <string> : Max. memory for adapter trimming (default: 12G).
== postalign bam settings
-mapq_thresh <int> : Threshold for low MAPQ reads removal (default: 30).
-rm_chr_from_tag <string> : Perl style reg-ex to exclude reads from tag-aligns. (example: 'other|ribo|mito|_', '_', default: blank)
-no_dup_removal <bool> : No dupe removal when filtering raw bam.
-wt_dedup <string> : Walltime for post-alignment filtering (default: 23h, 24:00:00).
-mem_dedup <string> : Max. memory for post-alignment filtering (default: 12G).
-dup_marker <string> : Dup marker for filtering mapped reaads in BAMs: picard or sambamba (default: picard).
-use_sambamba_markdup <bool> : Use sambamba markdup instead of Picard MarkDuplicates (default: false).
== postalign bed/tagalign settings
-mem_shuf <string> : Max. memory for UNIX shuf (default: 12G).
-fraglen0 <bool> : (LEGACY PARAM) Set predefined fragment length as zero for cross corr. analysis (add -speak=0 to run_spp.R).
-speak_xcor <int> : Set user-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to disable (default: -1).
-extra_param_xcor <string> : Set extra parameters for run_spp.R (cross-corr. analysis only).
== postalign bed/tagalign settings
-mem_shuf <string> : Max. memory for UNIX shuf (default: 12G).
-fraglen0 <bool> : (LEGACY PARAM) Set predefined fragment length as zero for cross corr. analysis (add -speak=0 to run_spp.R).
-speak_xcor <int> : Set user-defined cross-corr. peak strandshift (-speak= in run_spp.R). Use -1 to disable (default: -1).
-extra_param_xcor <string> : Set extra parameters for run_spp.R (cross-corr. analysis only).
== callpeak macs2 settings (requirements: -chrsz -gensz)
-gensz <string> : Genome size; hs for human, mm for mouse.
-wt_macs2 <string> : Walltime for MACS2 (default: 23h, 23:00:00).
-mem_macs2 <string> : Max. memory for MACS2 (default: 15G).
-extra_param_macs2 <string> : Extra parameters for macs2 callpeak.
== callpeak naive overlap settings
-nonamecheck <bool> : bedtools intersect -nonamecheck (bedtools>=2.24.0, use this if you get bedtools intersect naming convenction warnings/errors).
== callpeak etc settings
-npeak_filt <int> : # top peaks filtered from a narrow peak files (default: 500000).
== IDR settings
-idr_suffix <bool> : Append IDR threshold to IDR output directory.
== ATAQC settings
-tss_enrich <string> : TSS enrichment bed for ataqc.
-dnase <string> : DNase bed (open chromatin region file) for ataqc.
-prom <string> : Promoter bed (promoter region file) for ataqc.
-enh <string> : Enhancer bed (enhancer region file) for ataqc.
-reg2map <string> : Reg2map (file with cell type signals) for ataqc.
-reg2map_bed <string> : Reg2map_bed (file of regions used to generate reg2map signals) for ataqc.
-roadmap_meta <string> : Roadmap metadata for ataqc.
-mem_ataqc <string> : Max. memory for ATAQC (default: 20G).
-wt_ataqc <string> : Walltime for ATAQC (default: 47h, 47:00:00).