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Assay
7
RNA-seq
2
single cell isolation followed by RNA-seq
1
DNase-seq
1
whole genome sequencing assay
Pipeline status
1
active
Pipeline groups
1
DNase-seq Pipeline (ENCODE)
Software
2
BEDTools
MACS2
2
Samtools
1
BEDOPS
1
BWA
1
Bowtie 2
1
CoLo
1
Digital genomic footprinting
1
Picard
1
SRA_Toolkit
1
bedGraphToBigWig
1
bedToBigBed
1
cutadapt
1
getVariantOverlap.py
1
hotspot2
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
1
AMP-T2D consortium
analysis_steps.versions.software_versions.software.title!
MACS2
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Pipeline
DPL930NXT
active
DNase-seq Pipeline (ENCODE)
Assays:
DNase-seq
Software:
hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed