Hello,
I have the gene of the list of whole exome sequencing data from the paper. Can I use this list of genes to get the gene expression data? Should I download the transcriptomic data using this list of genes? How do I do that process? Also, can I get SNVs and CNVs data from those gene lists?
Thank you
Simply download the raw counts as .csv and process it using DESeq2 or limma-voom in R. For limma you will have to normalize your counts first. DESeq2 is easier. You will get log2FC values along with adj. p value. If you just want to check their expression for wet lab experiments. You can also calculate the fold change without checking for statistical significance. Just average the counts of control samples and experiment samples and FC= exp/control .
Thank you, but how to download the raw counts because I got the processed data from paper that mentioned only gene name?
@DeepyamanDas Thank you, but how to download the raw counts because I got the processed data from paper that mentioned only gene name?
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