This is a test version of Biostars. For the public version, visit https://www.biostars.org.
GEO RNA seq to DEG

Hi

I downloaded the RNA Seq data from the GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM3998167). I want to perform the DEG. The each txt file has around 66000 hits. The data processing information given is as under (Reads were cropped to 75bp using Trimmomatic Reads were mapped to GRCh38 (ensembl release 78) using STAR (v2.4.2a) Gene count tables were produced using HTSeq-count (v0.11.2) with -r pos -s reverse Genome_build: GRCh38, Ensembl release 78 Supplementary_files_format_and_content: txt files with gene-level counts).

My question is whether the data given is normalized or not. For my analysis i just log2 transform this data and perform further analysis. Is my approach right or I need to change it. Please suggest...

Regards

data geo sets
• 1,701 views • link
written by unislure • unislure

If you're starting with a count table (read counts to genes) the data is not normalized.

For my analysis i just log2 transform this data and perform further analysis.

What does your analysis consist of?

• 0 views • link
written by seidel seidel

Thanks for the reply

Differential expression, Correlation, multiple analysis

• 0 views • link
written by unislure • unislure

1 answer

Hi,

If you want to obtain DEGs, there's plenty of very good and easy to use R packages around, like DESEq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) or edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html), among others, and with very good manuals and tutorials over the internet.

For the input of these packages, all of what you need is the count table in the format that the package needs. (In your dataset it is the http download file at the end "GSE135251_RAW.tar", for all patients from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135251).

• 0 views • link
written by vitor • vitor

Log in to answer this question.

More posts like this