Hi, I downloaded RNAseq data and it is given with gene symbols. The RNAseq data was mapped to the human reference genome (NCBI/build37.2). I tried multiple ways to convert the gene symbols to refSeq hg38 IDs with no success, does anyone know how this can be done? Thanks in advance
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hilla.asida •
You can try NCBI Datasets for this. The web interface allows you to paste gene symbols for a species and returns the latest information about those genes in tabular format.
Thank you! Do you know if there is a way to download the total Gene table we get? I managed to download only 200 rows at a time, and I have 25,000 rows in total
Click on the checkbox to select all items and choose 'Download dataset' to download a package with data for all input rows. If you don't need sequence data, uncheck all three FASTA files and the downloaded package will still include a data_table.tsv file that contains information for all input genes. Note, the data in data_table.tsv file are represented on a per-transcript basis so you may see multiple rows for a single gene if it encodes multiple alternate splice variants.
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Please mind your genome versions (NCBI/build37.2 vs hg38 in OP)