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Assay
9
ChIP-seq
7
ATAC-seq
7
RNA-seq
4
Mint-ChIP-seq
3
DNase-seq
1
single cell isolation followed by RNA-seq
1
whole genome sequencing assay
Pipeline status
4
active
Pipeline groups
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
4
BEDTools
4
Bowtie 2
4
MACS2
4
Picard
4
Samtools
4
bedToBigBed
4
cutadapt
4
ptools_bin
4
sambamba
2
Irreproducible Discovery Rate (IDR)
2
Phantompeakqualtools
2
overlap_peaks.py
Developed by
4
AMP-T2D consortium
Showing 4 of 4 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