Search – Common Metabolic Diseases Genome Atlas

Showing 17 of 17 results

Pipeline
DPL269LNG
active
RNA-seq Pipeline 2 (Single-ended, ENCODE)
Assays: RNA-seq
Software: RNA pipelines, lrna-index-tophat, TopHat, Bowtie 2, lrna-align-tophat-se, Concat-fastq, Samtools, lrna-signals-unstranded, bedGraphToBigWig, STAR, lrna-signals, lrna-index-star, lrna-index-rsem, RSEM, lrna-align-star-se, lrna-quantification, lrna-mad-qc, Median Absolute Deviation
Pipeline
DPL009OFN
active
RNA-seq Pipeline 2 (Paired-ended, ENCODE)
Assays: RNA-seq
Software: RNA pipelines, lrna-index-tophat, TopHat, Bowtie 2, lrna-align-tophat-pe, Concat-fastq, Tophat BAM Repair, lrna-signals, bedGraphToBigWig, STAR, lrna-signals-stranded, lrna-index-star, lrna-index-rsem, RSEM, lrna-align-star-pe, Samtools, lrna-quantification, lrna-mad-qc, Median Absolute Deviation
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
DPL961ZQY
active
ATAC-seq Pipeline PLoS Genet. 2021-05-13;17(5):e100953
Assays: ATAC-seq
Software: Trim Galore, BWA, Samtools, Picard, MACS2
Pipeline
DPL930NXT
active
DNase-seq Pipeline (ENCODE)
Assays: DNase-seq
Software: hotspot2, BEDOPS, BWA, cutadapt, Samtools, Picard, Digital genomic footprinting, bedToBigBed
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
DPL707AXE
active
ATAC-seq Pipeline (ENCODE replicated)
Assays: ATAC-seq
Software: Bowtie 2, Samtools, Picard, cutadapt, sambamba, overlap_peaks.py, bedToBigBed, Irreproducible Discovery Rate (IDR), BEDTools, MACS2, Phantompeakqualtools
Pipeline
DPL121OYY
active
ATAC-seq Pipeline Gaulton Lab
Assays: ATAC-seq
Software: BWA, Samtools, Picard, MACS2, BEDTools
Pipeline
DPL779IGH
active
ATAC-seq Pipeline Cebola Lab (Hepatocytes)
Assays: ATAC-seq
Software: fastp, Bowtie 2, Samtools, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL741HGX
active
ATAC-seq Pipeline Cebola Lab
Assays: ATAC-seq
Software: fastp, Bowtie 2, Samtools, Picard, BEDTools, deepTools, MACS2, bedGraphToBigWig
Pipeline
DPL450NWL
active
RNA-seq Pipeline Cebola Lab
Assays: RNA-seq
Software: fastp, STAR, SALMON, Samtools, deepTools
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
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

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Showing 17 of 17 results