Assembly conversion of large BED files

Question

[bioinfo456]

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.

Answer 1

[Alex Reynolds]

UCSC liftOver: https://genome.ucsc.edu/cgi-bin/hgLiftOver

Run on the command-line to get around web file size restrictions.

Answer 2

[bernatgel]

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.

[bioinfo456]

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?

[bernatgel]

Yes, that's the one you need