RNA seq analysis differential expression analysis

Question

[bioinformatics]

Hi,

I'm trying to perform RNA sequencing differential expression analysis on the GEOdataset GSE111320 in the R program. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111320

Does anyone know how I might create one count file when the dataset has 40 xls.gz files?

Thank you

Answer 1

[benformatics]

I would say it's impossible given that the files attached to the experiments do not include counts by genes and instead are some sort of fusion annotation.

EDIT: So the solution is to download their raw FASTQ and do the rna-seq analysis manually

Answer 2

[ATpoint]

I do not know what these files contain. Anyway, use https://maayanlab.cloud/biojupies/analyze/search?q=gse111320&organism=all&sortby=new&min_samples=6&max_samples=500

BioJupies provides raw counts and metadata. Click through the early analysis and in the end you get a section to download the raw counts. Use that, won't get easier than that. BioJupies is great for that as it contains thousands of preprocessed datasets for a quick analysis. You can still download fastq from GEO later and process as you like if the data turn out to be useful for your question.