Hi all, I have a set of BED files containing certain peak locations obtained using NCBI Build GRCh37/UCSC Build hg19 genome assembly. I want the same in GRCh38 assembly. Ensembl's assembly convertor has an upload restriction of 50MB. Any alternate solutions please? Thanks.
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UCSC liftOver: https://genome.ucsc.edu/cgi-bin/hgLiftOver
Run on the command-line to get around web file size restrictions.
You can use liftOver in your computer with no restrictions.
We have used both the UCSC liftOver executable and the R Bioconductor liftOver function in the rtracklayer package and both have worked with no problems. In any case you will need a chain file for your specific conversion going from your your original assembly to your target assembly.
Thanks. Just to cross confirm, the chain file needed for the BED file conversion in my case is to be downloaded under Human genome -> (GRCh37/hg19) -> LiftOver files -> hg19ToHg38.over.chain.gz. Right?
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