Search – Common Metabolic Diseases Genome Atlas

Showing 9 of 9 results

Pipeline
DPL608JFY
active
TF ChIP-seq Pipeline 2 (ENCODE unreplicated)
Assays: ChIP-seq, Mint-ChIP-seq
Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, MACS2, BEDTools, Irreproducible Discovery Rate (IDR), Phantompeakqualtools, bedToBigBed
Pipeline
DPL935TZE
active
TF ChIP-seq Pipeline 2 (ENCODE replicated)
Assays: ChIP-seq, Mint-ChIP-seq
Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, MACS2, BEDTools, Irreproducible Discovery Rate (IDR), Phantompeakqualtools, bedToBigBed
Pipeline
DPL721SCW
active
Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)
Assays: ChIP-seq, Mint-ChIP-seq
Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, ptools_bin, overlap_peaks.py, bedToBigBed, MACS2, BEDTools
Pipeline
DPL064PJG
active
Histone ChIP-seq Pipeline 2 (ENCODE replicated)
Assays: ChIP-seq, Mint-ChIP-seq
Software: Bowtie 2, Samtools, sambamba, cutadapt, Picard, ptools_bin, MACS2, BEDTools, overlap_peaks.py, bedToBigBed
Pipeline
DPL118KGX
active
ChIP-seq Pipeline Ellinor Lab
Assays: ChIP-seq
Software: BWA, Picard, MACS2, BEDTools, ChromHMM
Pipeline
DPL245EPK
active
ChIP-seq Pipeline Cebola Lab
Assays: ChIP-seq
Software: fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL403RWM
active
ChIP-seq Pipeline (ENCODE)
Assays: ChIP-seq
Software: Bowtie 2, Samtools, sambamba, Picard, cutadapt, MACS2, BEDTools, overlap_peaks.py, bedToBigBed
Pipeline
DPL983WYV
active
ChIP-Atlas Pipeline
Assays: ChIP-seq, DNase-seq
Software: SRA_Toolkit, Bowtie 2, Samtools, BEDTools, bedGraphToBigWig, MACS2, unknown, CoLo
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

Assay

Pipeline status

Pipeline groups

Software

Developed by

Showing 9 of 9 results