Existing Pipelines

Contents:

• 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
• scRNA-seq
  • Check Reads check_reads
  • Genome Indexing hisat_indexing/star_indexing
  • Quality Check fastqc
  • Whitelist whitelist
  • Extract extract
  • Read Mapping hisat_mapping/star_mapping
  • Reformat Reference gtftobed
  • Mapping Quality rseqc
  • Quantification counting
  • Summary Report multiqc
• DGE
  • Quantification counting
  • Expression Matrix expression_matrix
  • Sample Renaming rename_samples
  • Summary Report multiqc