Conversion of gene symbol to refSeqID

Question

[hilla.asida]

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

[cpad0112]

Please mind your genome versions (NCBI/build37.2 vs hg38 in OP)

Answer 1

[vkkodali_ncbi]

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.

[hilla.asida]

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

[vkkodali_ncbi]

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.