Skip to content

README.md

Latest commit

 

History

History
22 lines (12 loc) · 549 Bytes

README.md

File metadata and controls

22 lines (12 loc) · 549 Bytes

General Pipeline for RNAseq

  • Fastqc > STAR_2.7.8a > Samtools(1.21)Index > htseq_2.0.7 > Deseq2

  • Fastqc > STAR_2.7.8a > Samtools(1.21)Index > RSEM > Deseq2

  • Fastqc > STAR_2.7.8a > Samtools(1.21)Index > feature_counts > Deseq2

  • Fastqc > HISAT2 > Samtools(1.21)Index > feature_counts > Deseq2

  • Fastqc > HISAT2 > Samtools(1.21)Index > htseq > Deseq2

Quality Trimming depending on library preparation protocol:

  1. Trimmomatic
  2. Fastp
  3. Cutadapt
  4. BBDuK

3' and 5' bias detection tools - Picard CollectRnaSeqMetrics, RNAseqQC