A pipeline for RNA-Seq analysis

I need a pipline for analyzing RNA-seq Fastq.gz file. I have started with Fastq.QC. I have also used the Bowtie2 and converted the Fastq.gz to BAM format. However, I need to have the read counts. Any help in this step, please.

Hi Fatemeh

Have a look at the extensive training material:

In particular: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html

Hope this helps, Hans-Rudolf

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