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Assay
5
ChIP-seq
4
Mint-ChIP-seq
2
ATAC-seq
1
DNase-seq
Pipeline status
2
active
Pipeline groups
1
ATAC-seq Pipeline (ENCODE replicated)
1
ATAC-seq Pipeline (ENCODE unreplicated)
Software
7
MACS2
6
BEDTools
6
Samtools
5
Picard
4
Bowtie 2
2
BWA
2
Irreproducible Discovery Rate (IDR)
2
bedGraphToBigWig
2
bedToBigBed
2
cutadapt
2
deepTools
2
fastp
2
overlap_peaks.py
2
sambamba
1
Phantompeakqualtools
1
Trim Galore
1
getVariantOverlap.py
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
Developed by
2
AMP-T2D consortium
Showing 2 of 2 results
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Pipeline
DPL707AXE
active
ATAC-seq Pipeline (ENCODE replicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, overlap_peaks.py, bedToBigBed, Irreproducible Discovery Rate (IDR), BEDTools, MACS2, Phantompeakqualtools
Pipeline
DPL967MZM
active
ATAC-seq Pipeline (ENCODE unreplicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, Irreproducible Discovery Rate (IDR), overlap_peaks.py, MACS2, BEDTools, bedToBigBed