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Assay
1
DNase-seq
Pipeline status
1
active
Pipeline groups
1
DNase-seq Pipeline (ENCODE)
Software
16
Samtools
14
MACS2
13
BEDTools
12
Bowtie 2
11
Picard
8
bedToBigBed
8
cutadapt
7
bedGraphToBigWig
7
sambamba
6
STAR
5
RSEM
5
overlap_peaks.py
4
BWA
4
Irreproducible Discovery Rate (IDR)
4
ptools_bin
3
Phantompeakqualtools
3
deepTools
3
fastp
2
Concat-fastq
2
Median Absolute Deviation
2
RNA pipelines
2
TopHat
2
lrna-index-rsem
2
lrna-index-star
2
lrna-index-tophat
2
lrna-mad-qc
2
lrna-quantification
2
lrna-signals
1
Association testing and fine mapping: eQTL-Catalogue/qtlmap
1
BEDOPS
1
ChromHMM
1
CoLo
1
Digital genomic footprinting
1
Gene expression QC and normalisation: eQTL-Catalogue/qcnorm
1
Genotype QC and imputation: eQTL-Catalogue/genimpute
1
RNA-seq quantification: eQTL-Catalogue/rnaseq
1
SALMON
1
SRA_Toolkit
1
Tophat BAM Repair
1
Trim Galore
1
getVariantOverlap.py
1
hotspot2
1
lrna-align-star-pe
1
lrna-align-star-se
1
lrna-align-tophat-pe
1
lrna-align-tophat-se
1
lrna-signals-stranded
1
lrna-signals-unstranded
1
makeCandidateRegions.py
1
predict.py
1
run.neighborhoods.py
1
unknown
Developed by
1
AMP-T2D consortium
title!
ATAC-seq Pipeline Cebola Lab
Showing 1 of 1 results
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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