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Assay
1
ATAC-seq
1
DNase-seq
1
RNA-seq
Pipeline status
2
active
Pipeline groups
1
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
DNase-seq Pipeline (ENCODE)
Software
8
MACS2
8
Samtools
BEDTools
6
Picard
5
Bowtie 2
3
BWA
3
bedGraphToBigWig
3
bedToBigBed
3
cutadapt
2
Irreproducible Discovery Rate (IDR)
2
deepTools
2
fastp
2
overlap_peaks.py
2
sambamba
1
BEDOPS
1
CoLo
1
Digital genomic footprinting
1
Phantompeakqualtools
1
SRA_Toolkit
1
Trim Galore
1
getVariantOverlap.py
1
hotspot2
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
0
lrna-align-tophat-pe
Developed by
1
AMP-T2D consortium
1
Kyle Gaulton, UCSD
analysis_steps.versions.software_versions.software.title!
BEDTools
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Pipeline
DPL961ZQY
active
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
Assays:
ATAC-seq
Software:
Trim Galore, BWA, Samtools, Picard, MACS2
Pipeline
DPL930NXT
active
DNase-seq Pipeline (ENCODE)
Assays:
DNase-seq
Software:
hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed