NCBI's GRCh38 and UCSC's hg38

When we upload the fastq via ftp in Galaxy there is drop down menu for selecting Genome, I want to select GRCH38 for bulk seq, which option I should select from drop down menus from several options.

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Welcome @kanwarjag

GRCH38 is the NCBI version of UCSC’s hg38 human genome.

The UCSC version is what you’ll find indexed for tools on most public Galaxy servers.

Fastq data doesn’t necessarily need to have a genome build assigned (“database”). But if your plan is to map against the hg38 genome, then you could assign this database and all will be a match:

More about the genome builds and how to avoid problems with chromosome identifiers between inputs and build-in indexes is in this FAQ: https://galaxyproject.org/support/

Thanks!