Omics Pipe Available Pipelines
RNA-seq (Tuxedo)
- RNA-seq Tuxedo Modules
- Modules included in the Tuxedo RNA-seq pipeline.
- FASTQC
- TopHat
- Cufflinks
- Cuffmerge
- Cuffmergetocompare
- Cuffdiff
- R Summary Report - CummeRbund
RNA-seq(Anders 2013)
- RNA-seq Count Based Modules
- Modules included in the count-based RNA-seq pipeline.
- FASTQC
- STAR
- HTSEQ
- R Summary Report - DESEQ2
Whole Exome Sequencing (GATK)
- Whole Genome and Whole Exome Sequencing Modules
- Modules included in the whole exome sequencing pipeline.
- FASTQC
- BWA-MEM
- PICARD Mark Duplicates
- GATK Preprocessing
- GATK Variant Discovery
- GATK Variant Filtering
Whole Genome Sequencing (GATK)
- Whole Genome and Whole Exome Sequencing Modules
- Modules included in the whole genome sequencing pipeline.
- FASTQC
- BWA-MEM
- PICARD Mark Duplicates
- GATK Preprocessing
- GATK Variant Discovery
- GATK Variant Filtering
ChIP-seq (MACS)
- ChIP-seq Modules – MACS
- Modules included in the ChIP-seq MACS pipeline.
- FASTQC
- Homer ChIP Trim
- Bowtie
- MACS
ChIP-seq (HOMER)
- ChIP-seq Modules – HOMER
- Modules included in the ChIP-seq HOMER pipeline.
- FASTQC
- Homer ChIP Trim
- Bowtie
- Homer Read Density
- Homer Peaks
- Homer Peak Track
- Homer Annotate Peaks
- Homer Find Motifs
TCGA Reanalysis Pipeline - RNAseq Counts
- RNA-seq Count Based Modules- TCGA
- Modules included in the RNAseq counts pipeline for TCGA reanalysis.
- TCGA Download (GeneTorrent)
- FASTQC
- STAR
- HTSEQ
- Report
miRNAseq Counts (Anders 2013)
- miRNA-seq Count Based Modules
- Modules included in the miRNAseq counts pipeline.
- Cutadapt
- FASTQ Length Filter
- FASTQC
- STAR
- HTSEQ
- Report
miRNAseq (Tuxedo)
- miRNA-seq Tuxedo Modules
- Modules included in the miRNAseq Tuxedo pipeline.
- Cutadapt
- FASTQ Length Filter
- TopHat
- Cufflinks
- Cuffmerge
- Cuffmergetocompare
- Cuffdiff
- R Summary Report
