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Assay
9
ChIP-seq
7
ATAC-seq
7
RNA-seq
4
Mint-ChIP-seq
3
DNase-seq
2
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
7
active
Pipeline groups
1
ATAC-seq Pipeline (ENCODE replicated)
1
ATAC-seq Pipeline (ENCODE unreplicated)
1
ATAC-seq Pipeline Cebola Lab
1
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
1
ATAC-seq Pipeline Gaulton Lab
1
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
Activity by Contact
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
3
AMP-T2D consortium
2
Ines Cebola, Imperial College London
2
Kyle Gaulton, UCSD
Showing 7 of 7 results
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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
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
DPL121OYY
active
ATAC-seq Pipeline Gaulton Lab
Assays:
ATAC-seq
Software:
BWA, Samtools, Picard, MACS2, BEDTools
Pipeline
DPL779IGH
active
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
Assays:
ATAC-seq
Software:
fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL741HGX
active
ATAC-seq Pipeline Cebola Lab
Assays:
ATAC-seq
Software:
fastp, Bowtie 2, Samtools, Picard, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL010CNP
active
Activity by Contact
Assays:
ATAC-seq, ChIP-seq, DNase-seq
Software:
MACS2, BEDTools, makeCandidateRegions.py, run.neighborhoods.py, predict.py, getVariantOverlap.py
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