1) Introduction:

This is a simple preprocessing tool to merge individual gene count files (Eg. output count files from htseq)

NOTE: first column must contain the genes. If the gene columns do not match in all files, this tool will not work


Features
  • Merge individual sample count files. See Sample Input Files below for more details
  • Or merge multiple matrices
  • Convert ensembl gene IDs to gene names
    • Option to choose from available genome/versions
    • If genome/version is not available in the options and you have a .gtf file for your genome follow these instructions.
  • Option to add pseudocounts (+1)
  • Download merged counts file in .csv format
  • Transcriptome Analysis (Optional) after merging your counts:
    • Use our Seurat Wizard to carry out single-cell RNA analysis
    • Use DESeq2Shiny or START apps to carry out bulk RNA analysis
    • If there are NO replicates , use DESeq2Shiny app for exploratory analysis

2) Sample Input Files:

Select multiple files to upload, E.g. Input files:

File 1 of 8: CT6_1.txt

File 2 of 8: CT6_2.txt

etc ...

Note: File names will be used as sample (column) names in output table. You can edit the column names after merging


3) Sample Output File:

Output depending on options selected:

A) Without renaming/converting genes (Default)


B) Retrieve gene names (replace), E.g. output file


C) Retrieve gene names (add), E.g. output file


4) Transcriptome Analysis (Optional):

Start your analysis by launching the appropriate application for your data

Your merged counts data will be automatically loaded


Merged counts


Sample names are NOT valid for use in our analysis apps

Edit the column names so they are of the following format:

  • sampleName_replicateNumber. Eg: kidneyA_1, kidneyA_2, liver_1, liver_2, etc ...
  • do NOT use any special characters in sample names except underscore'_' to denote replicate numbers

Download Merged File