Prepare Input files

To use this pipeline, users should prepare the raw read sequences with or without biological replicate in fastq format first. In addition, we recommend our users to use the paired-end sequences and the sequencing depth should be more than 70M. The length of the reads should be longer than 50bp, and longer than 100bp is the best.

To use the five kinds of software and annotation, users should choose an appropriate reference index as one of the input files. If users don’t provide a specific index file, the pipeline will use Hg19 index file by default.

For the step of differential gene expression analysis, users should provide design.txt as a design file and compare.txt as a compare file.

The parameters of each input file are described in the section of Parameters in detail, users can refer to that section and choose the input files as their specific needs.

Input file

• design.txt

  sampleInfor presents the experimental design of your data set, it is just like a design file of DESeq2 and EdgeR input.

  Sample  Type
  P1003NA N
  P1003TA T
  P1162NA N
  P1162TA T
  P1408NA N
  P1408TA T
  P1527NA N
  

• compare.txt specify which group to compare in your differential expression analysis

  T_vs_N
  

  T and N are the identical strings as the Type column in design.txt.