atac-seq-pipeline
Link to section 'Introduction' of '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.
Docker hub: https://hub.docker.com/r/encodedcc/atac-seq-pipeline
Home page: https://www.encodeproject.org/atac-seq/
Link to section 'Versions' of 'atac-seq-pipeline' Versions
- 2.1.3
Link to section 'Commands' of 'atac-seq-pipeline' 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
Link to section 'Module' of 'atac-seq-pipeline' Module
You can load the modules by:
module load biocontainers
module load atac-seq-pipeline
Link to section 'Example job' of 'atac-seq-pipeline' Example job
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