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Assay
8
ChIP-seq
6
RNA-seq
5
ATAC-seq
4
Mint-ChIP-seq
3
DNase-seq
2
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
8
active
Pipeline groups
1
Activity by Contact
1
ChIP-Atlas Pipeline
1
ChIP-seq Pipeline (ENCODE)
1
ChIP-seq Pipeline Ellinor Lab
1
Histone ChIP-seq Pipeline 2 (ENCODE replicated)
1
Histone ChIP-seq Pipeline 2 (ENCODE unreplicated)
1
TF ChIP-seq Pipeline 2 (ENCODE replicated)
1
TF ChIP-seq Pipeline 2 (ENCODE unreplicated)
Software
9
BEDTools
9
MACS2
7
Bowtie 2
7
Samtools
6
Picard
5
bedToBigBed
5
cutadapt
5
sambamba
4
ptools_bin
3
overlap_peaks.py
2
Irreproducible Discovery Rate (IDR)
2
Phantompeakqualtools
2
bedGraphToBigWig
1
BWA
1
ChromHMM
1
CoLo
1
SRA_Toolkit
1
deepTools
fastp
1
getVariantOverlap.py
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
7
AMP-T2D consortium
1
Patrick T. Ellinor, Broad
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fastp
Showing 8 of 8 results
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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
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