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Assay
1
ATAC-seq
1
ChIP-seq
1
Mint-ChIP-seq
Pipeline status
2
active
Pipeline groups
1
ATAC-seq Pipeline (ENCODE replicated)
1
ATAC-seq Pipeline (ENCODE unreplicated)
1
DNase-seq Pipeline (ENCODE)
1
RNA-seq Pipeline 2 (Paired-ended, ENCODE)
1
TF ChIP-seq Pipeline 2 (ENCODE replicated)
1
TF ChIP-seq Pipeline 2 (ENCODE unreplicated)
Software
2
BEDTools
2
Bowtie 2
2
Irreproducible Discovery Rate (IDR)
2
MACS2
2
Picard
2
Samtools
2
bedToBigBed
2
cutadapt
2
sambamba
1
Phantompeakqualtools
1
overlap_peaks.py
1
ptools_bin
0
BEDOPS
0
lrna-align-tophat-pe
Developed by
2
AMP-T2D consortium
Showing 2 of 2 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
DPL967MZM
active
ATAC-seq Pipeline (ENCODE unreplicated)
Assays:
ATAC-seq
Software:
Bowtie 2, Samtools, Picard, cutadapt, sambamba, Irreproducible Discovery Rate (IDR), overlap_peaks.py, MACS2, BEDTools, bedToBigBed