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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.

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