Pipeline steps

• Quality statistics (fastq level)
  • fastqc
  • htseq-qa
  • fastp (fastqc, htseq-qa)
• Remove adapters (5', 3' polyA tail)
  • cutadapt
  • fastp
• Create index for mapping
  • STAR
• Map reads
  • STAR
    • add feature two-pass mode
    • multimappers
    • End to End
• Quality statistics (bam level)
  • ALFA (https://github.com/biocompibens/ALFA)
• Estimate gene/transcript expression
  • salmon on fastq file
  • kallisto on fastq file
• Summary
  • Create gene expression table of
  • TPM
  • Normalized (raw) reads
  • multiqc