Atac-seq-pipeline

Introduction

The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment. It was developed by Anshul Kundaje’s lab at Stanford University.

For more information, please check:
Docker hub: https://hub.docker.com/r/encodedcc/atac-seq-pipeline
Home page: https://www.encodeproject.org/atac-seq/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.1.3

BELL

2.1.3

GAUTSCHI

2.1.3

NEGISHI

2.1.3

SCHOLAR

2.1.3

Commands

  • 10x_bam2fastq

  • SAMstats

  • SAMstatsParallel

  • ace2sam

  • aggregate_scores_in_intervals.py

  • align_print_template.py

  • alignmentSieve

  • annotate.py

  • annotateBed

  • axt_extract_ranges.py

  • axt_to_fasta.py

  • axt_to_lav.py

  • axt_to_maf.py

  • bamCompare

  • bamCoverage

  • bamPEFragmentSize

  • bamToBed

  • bamToFastq

  • bed12ToBed6

  • bedToBam

  • bedToIgv

  • bed_bigwig_profile.py

  • bed_build_windows.py

  • bed_complement.py

  • bed_count_by_interval.py

  • bed_count_overlapping.py

  • bed_coverage.py

  • bed_coverage_by_interval.py

  • bed_diff_basewise_summary.py

  • bed_extend_to.py

  • bed_intersect.py

  • bed_intersect_basewise.py

  • bed_merge_overlapping.py

  • bed_rand_intersect.py

  • bed_subtract_basewise.py

  • bedpeToBam

  • bedtools

  • bigwigCompare

  • blast2sam.pl

  • bnMapper.py

  • bowtie2sam.pl

  • bwa

  • chardetect

  • closestBed

  • clusterBed

  • complementBed

  • compress

  • computeGCBias

  • computeMatrix

  • computeMatrixOperations

  • correctGCBias

  • coverageBed

  • createDiff

  • cutadapt

  • cygdb

  • cython

  • cythonize

  • deeptools

  • div_snp_table_chr.py

  • download_metaseq_example_data.py

  • estimateReadFiltering

  • estimateScaleFactor

  • expandCols

  • export2sam.pl

  • faidx

  • fastaFromBed

  • find_in_sorted_file.py

  • flankBed

  • gene_fourfold_sites.py

  • genomeCoverageBed

  • getOverlap

  • getSeq_genome_wN

  • getSeq_genome_woN

  • get_objgraph

  • get_scores_in_intervals.py

  • gffutils-cli

  • groupBy

  • gsl-config

  • gsl-histogram

  • gsl-randist

  • idr

  • int_seqs_to_char_strings.py

  • interpolate_sam.pl

  • intersectBed

  • intersection_matrix.py

  • interval_count_intersections.py

  • interval_join.py

  • intron_exon_reads.py

  • jsondiff

  • lav_to_axt.py

  • lav_to_maf.py

  • line_select.py

  • linksBed

  • lzop_build_offset_table.py

  • mMK_bitset.py

  • macs2

  • maf_build_index.py

  • maf_chop.py

  • maf_chunk.py

  • maf_col_counts.py

  • maf_col_counts_all.py

  • maf_count.py

  • maf_covered_ranges.py

  • maf_covered_regions.py

  • maf_div_sites.py

  • maf_drop_overlapping.py

  • maf_extract_chrom_ranges.py

  • maf_extract_ranges.py

  • maf_extract_ranges_indexed.py

  • maf_filter.py

  • maf_filter_max_wc.py

  • maf_gap_frequency.py

  • maf_gc_content.py

  • maf_interval_alignibility.py

  • maf_limit_to_species.py

  • maf_mapping_word_frequency.py

  • maf_mask_cpg.py

  • maf_mean_length_ungapped_piece.py

  • maf_percent_columns_matching.py

  • maf_percent_identity.py

  • maf_print_chroms.py

  • maf_print_scores.py

  • maf_randomize.py

  • maf_region_coverage_by_src.py

  • maf_select.py

  • maf_shuffle_columns.py

  • maf_species_in_all_files.py

  • maf_split_by_src.py

  • maf_thread_for_species.py

  • maf_tile.py

  • maf_tile_2.py

  • maf_tile_2bit.py

  • maf_to_axt.py

  • maf_to_concat_fasta.py

  • maf_to_fasta.py

  • maf_to_int_seqs.py

  • maf_translate_chars.py

  • maf_truncate.py

  • maf_word_frequency.py

  • makeBAM.sh

  • makeDiff.sh

  • makeFastq.sh

  • make_unique

  • makepBAM_genome.sh

  • makepBAM_transcriptome.sh

  • mapBed

  • maq2sam-long

  • maq2sam-short

  • maskFastaFromBed

  • mask_quality.py

  • mergeBed

  • metaseq-cli

  • multiBamCov

  • multiBamSummary

  • multiBigwigSummary

  • multiIntersectBed

  • nib_chrom_intervals_to_fasta.py

  • nib_intervals_to_fasta.py

  • nib_length.py

  • novo2sam.pl

  • nucBed

  • one_field_per_line.py

  • out_to_chain.py

  • pairToBed

  • pairToPair

  • pbam2bam

  • pbam_mapped_transcriptome

  • pbt_plotting_example.py

  • peak_pie.py

  • plot-bamstats

  • plotCorrelation

  • plotCoverage

  • plotEnrichment

  • plotFingerprint

  • plotHeatmap

  • plotPCA

  • plotProfile

  • prefix_lines.py

  • pretty_table.py

  • print_unique

  • psl2sam.pl

  • py.test

  • pybabel

  • pybedtools

  • pygmentize

  • pytest

  • python-argcomplete-check-easy-install-script

  • python-argcomplete-tcsh

  • qv_to_bqv.py

  • randomBed

  • random_lines.py

  • register-python-argcomplete

  • sam2vcf.pl

  • samtools

  • samtools.pl

  • seq_cache_populate.pl

  • shiftBed

  • shuffleBed

  • slopBed

  • soap2sam.pl

  • sortBed

  • speedtest.py

  • subtractBed

  • table_add_column.py

  • table_filter.py

  • tagBam

  • tfloc_summary.py

  • ucsc_gene_table_to_intervals.py

  • undill

  • unionBedGraphs

  • varfilter.py

  • venn_gchart.py

  • venn_mpl.py

  • wgsim

  • wgsim_eval.pl

  • wiggle_to_array_tree.py

  • wiggle_to_binned_array.py

  • wiggle_to_chr_binned_array.py

  • wiggle_to_simple.py

  • windowBed

  • windowMaker

  • zoom2sam.pl

Module

You can load the modules by:

module load biocontainers
module load atac-seq-pipeline

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run atac-seq-pipeline on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=atac-seq-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers atac-seq-pipeline

# Your atac-seq-pipeline workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=atac-seq-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers atac-seq-pipeline

# Your atac-seq-pipeline workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=atac-seq-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers atac-seq-pipeline

# Your atac-seq-pipeline workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=atac-seq-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers atac-seq-pipeline

# Your atac-seq-pipeline workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=atac-seq-pipeline
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers atac-seq-pipeline

# Your atac-seq-pipeline workflow...