How to execute the RNA-Seq FASTQ file processing ~ Data import to Subio Platform

Subio Platform accepts FASTQ files of RNA-Seq data. It utilizes a pipeline composed of fastp , HISAT2, and StringTie  on both Mac and Windows10 computers. You don't need a workstation nor UNIX command-line skills. It works on an ordinary Windows or Mac computer. This is the easiest and cheapest way to build an RNA-Seq data processing environment on the Windows system. Even for who can use the command-line tools, doing it with the Subio Platform is more comfortable. Moreover, StringTie output is only TPM and you have to run prepDE.py to calculate read counts. If you process FASTQ files with Subio Platform, you can get both TPM and read counts effortlessly. It is crucial to use read counts for filtering noise out, and TPM for the subsequent statistical analysis. Otherwise, you will easily lead the wrong conclusions.

Before you run the pipe, you have to install and setup these tools. If you have any difficulties in the installation, please order the RNA-Seq Data Analysis Support Service.

Instruction - How to import RNA-Seq FASTQ files

Have the FASTQ files to import as .gz archived files. It generates intermediate results in the same folder, so be sure that there is enough free disk space, which is at least five times larger than the total size of the FASTQ files before you start executing. The process will stop in the middle if there is no disk space available. The FASTQ file directory can be on an external disk.

If you have paired-end FASTQ files, please follow the rule of file names.

If you have been using the Subio Platform from v1.23 or previous versions, please create a platform of Ensebml genes by following this instruction before this tutorial.

Importing RNA-Seq FASTQ files

After this, please go forward to the next tutorial of how to analyze the gene expression data by RNA-Seq.