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Assay
5
RNA-seq
3
ATAC-seq
2
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2
DNase-seq
2
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
3
active
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1
ATAC-seq Pipeline Gaulton Lab
1
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
1
Activity by Contact
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7
MACS2
6
BEDTools
6
Samtools
5
Picard
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2
BWA
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Irreproducible Discovery Rate (IDR)
2
bedGraphToBigWig
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bedToBigBed
2
cutadapt
2
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2
fastp
2
overlap_peaks.py
2
sambamba
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1
Trim Galore
1
getVariantOverlap.py
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
Developed by
2
Kyle Gaulton, UCSD
1
AMP-T2D consortium
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Bowtie 2
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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
DPL121OYY
active
ATAC-seq Pipeline Gaulton Lab
Assays:
ATAC-seq
Software:
BWA, Samtools, Picard, MACS2, BEDTools
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