3.1 - TopHat/Hisat2 & Cufflinks protocol
To complete this protocol using the pipeline mode, remember that you will need the following material:
- The 10 fastq files for the PVL group (From JVB-R1 to JVB-R10)
- The 5 fastq files for the control group (From JVB-R11 to JVB-R15)
- The fasta file with the GRCh38.95 reference genome and its associated GTF file.
When you have this material ready, you can access the pipeline designer interface (RNAseq Protocols → Pipeline mode) and proceed as indicated in video 9
Video 9. Tophat/Hisat2 & Cufflinks protocol for differential expression analysis executed using pipeline mode of RNASeq.
|
Expected results from the Tophat/Hisat2 & Cufflinks protocol using the Pipeline execution mode: When the pipeline mode is complete, you will receive the results of differential
expression sample with the reads mapped against the reference genome. The expected results of this step are available in the following link Pipeline mode: Tophat/Hisat2 & Cufflinks protocol Remember you can check if the job was successfully completed by accessing the job tracking panel of RNASeq. To learn more about any tool used in the pipeline and their outputs see their respective manuals, referred in previous sections of this tutorial. |
|---|
