By Yan Li

PhD in Bioinformatics, University of Liverpool



Popular software

  • Mapping: Tophat2, HISAT2
  • Reads counting: HTSeq-counts, Cufflink
  • Defferential Expressing analysis: EdgeR, DEseq2, limma
  • GO enrichment: DAVID, g.profiler


  • RPKM: Reads Per Kilobase per Million mapped read.
    • RPKM = 10^9 * N / L * 1 / C
    • N: the total number of reads mapped to a transcript
    • C: the number of reads mapped to a gene
    • L: the length of the gene
  • GO: Gene ontology

Basic Statistics

  • P-value and False discovery rate (FDR) adjusted p values
    • a p-value of 0.05 implies that 5% of all tests will result in false positives.
    • An FDR adjusted p-value (or q-value) will result in fewer false positives.
  • Fold Change
    • Fold change is a measure describing how much a quantity changes going from an initial to a final value.

Demonstration and Workshop