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