I have installed the all Softwares in Linux and Raw seq files in Fastq format and reference seq in Fasta and GTF format. I can't run the commands in Linux terminal for alignment and the mapping of reads to genes and differential expression.
There are many ways to do this depending on your exact needs. Which tools have you installed? Do you have experience with Linux previously? If not, you may want to check out Galaxy (https://usegalaxy.org/), which is a web-based platform that has most of the tools you'll need for these sorts of analyses. I believe they also have some workflows mapped out for you, although I haven't used these myself.
I think there is not a simple tutorial for RNAseq differential expression, there is plenty of methods, packages, and workflows.
Anyway, for the quality control of FASTQ files, you've to start by studying the FASTQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), understanding the concepts of trimming etc.
Then you can start by studying the alignment, there are several aligners, STAR, HiSat (here a review https://www.mdpi.com/2075-4426/9/2/18/pdf).
I don't suggest to do this on your own machine, unless you have a very high performing computer...
Then, you can quantify, obtaining the count matrix, in R you can use featureCounts function in the rsubread package.
Finally, you can start by following this article (there is also the detailed code for the pipeline in R), which will be helpful in your situation!
Article RNA-Seq workflow: Gene-level exploratory analysis and differ...
Of course, this is only ONE of the possible solutions... But it's a starting point :)
you may find a very good tutoral here:
https://research.csc.fi/rnaseq-tutorial
The authors described whole procedure step-by-step and provided the sample data for the analyses
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