Transform Bedgraph counts into Gene Counts (DESeq2 input)

Question

[LuisNagano]

Hello guys, I downloaded some raw RNA-seq data from GEO, but they came in the bedgraph format with the counts. I would like to transform that bedgraph into gene counts to analyze in DESeq2. Does anyone know how to do this?

chr1    14322   14350   2.34
chr1    14350   14351   3.51
chr1    14351   14358   4.68
chr1    14358   14360   8.19
chr1    14360   14361   9.36
chr1    14361   14364   12.87

Thank you!

[ATpoint]

RNA-seq is based on integer counts so a file with floats cannot be raw data. Better download raw fastq files and analyze yourself. For raw data see e.g. Fast download of FASTQ files and metadata from the European Nucleotide Archive (ENA)

Answer 1

[gocougs]

Hello!

I downloaded some raw RNA-seq data from GEO, but they came in the bedgraph format

I don't think this would be considered raw data. You would need to download the fastq files from the Short-Read Archive at NCBI.

Would you mind sharing the GEO # and I'll see if they provided other processed files? You may be able to just download the expression data directly if the uploaders provided it.

[LuisNagano]

Thank you, Gocougs, I guess that values are FPKM or RPM values, right?! but I want the gene symbols of that bedgraph files. How do I convert chromosomal coordinates into Gene Symbols/Ensembl_ids?

chr1    17434   17439
chr1    17439   17440
chr1    17440   17443

The GSE number is GSE118530