Pipeliner DocumenationΒΆ
- Requirements
- Basic Usage
- Pipeline Structure
- Existing Pipelines
- RNA-seq
- Check Reads
check_reads
- Genome Indexing
hisat_indexing/star_indexing
- Pre-Quality Check
pre_fastqc
- Pre-MultiQC
pre_multiqc
- Read Trimming
trim_galore
- Read Mapping
hisat_mapping/star_mapping
- Reformat Reference
gtftobed
- Mapping Quality
rseqc
- Quantification
counting
- Expression Matrix
expression_matrix
- Expression Features
expression_features
- Expression Set
expression_set
- Summary Report
multiqc
- Check Reads
- scRNA-seq
- DGE
- RNA-seq
- Extending Pipelines