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!
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LuisNagano •
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.
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
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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)