Miscellaneous Processes

This section contains various utility and miscellaneous processes.

Process	Description
Adapter Removal	Remove adapters
Add Custom Seq to Genome GTF	Add custom sequence
ATAC CHIP Summary	ATAC/CHIP summary
ATAC MACS	ATAC MACS peak calling
ATAC Prep	ATAC preparation
BAM Sort Index	Sort and index BAM
BAM to FASTQ	Convert BAM to FASTQ
BBMap BBmerge	BBMap BBmerge
Bed Merge	Merge BED files
Bedtools Coverage	Bedtools coverage
Bowtie Summary	Bowtie summary
CellRanger FASTQ Prep	CellRanger FASTQ prep
ChIP ATAC seq Reporting	ChIP/ATAC reporting
ChIP MACS	ChIP MACS peak calling
ChIP Prep	ChIP preparation
Cluster Analysis	Cluster analysis
Convert GTF Attributes	Convert GTF attributes
DanceMapper	DanceMapper analysis
Deduplication Summary	Deduplication summary
deepTools CreateMatrix	Create deepTools matrix
deepTools PlotHeatmap	Plot deepTools heatmap
Detect Library Type	Detect library type
FASTQ Dump Collection Parser	Parse FASTQ dump collection
FASTQ Dump	FASTQ dump
File to Set Conversion for H5	Convert file to set (H5)
File to Set Conversion for Reads	Convert file to set (reads)
Genome Browser	Genome browser
HISAT2 Summary	HISAT2 summary
HOMER Annotate Peaks	HOMER peak annotation
HOMER Motif Finder	HOMER motif finder
IGV BAM2TDF Converter	IGV BAM to TDF
Kallisto Alignment Summary	Kallisto alignment summary
Kallisto Summary	Kallisto summary
Kallisto Transcript to Gene Count	Kallisto transcript to gene
Liftoff	Liftoff annotation
Merge BAM	Merge BAM files
Merge BAM and Sort Index	Merge, sort and index BAM
Merge TSV Files	Merge TSV files
MIMseq Groups	MIMseq groups
Overall Summary	Overall summary
Prepare DESeq2	Prepare DESeq2
Prepare Input Velocyto	Prepare velocyto input
Prepare LimmaVoom	Prepare Limma-Voom
Quality Filtering	Quality filtering
Remove Multimappers with Samtools	Remove multimappers
RNAFramework Combine	RNAFramework combine
RNAFramework Count	RNAFramework count
RNAFramework Fold	RNAFramework fold
RNAFramework Map	RNAFramework map
RNAFramework Norm	RNAFramework normalize
RSEM Alignment Summary	RSEM alignment summary
RSEM Count	RSEM count
Run Markdown	Run markdown
Salmon Alignment Summary	Salmon alignment summary
Salmon Summary	Salmon summary
Salmon Transcript to Gene Count	Salmon transcript to gene
Samtools	Samtools utilities
Sequential Mapping BAM Count	Sequential mapping BAM count
Sequential Mapping Summary	Sequential mapping summary
ShapeMapper	ShapeMapper
STAR Summary	STAR summary
Trimmer	Trimmer
UCSC BAM2BigWig Converter	BAM to BigWig
UMI Extract	UMI extraction
VEP	Variant Effect Predictor