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:

Versions

  • 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 -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
ml biocontainers atac-seq-pipeline