Create Chain File for Converting Genome Coordinates

Question: Create Chain File for Converting Genome Coordinates

14 months ago by

Gabriel • 30 wrote:

I was wondering about options for creating the "chain" file for converting genome coordinates from one genome assembly to another. Malachi Griffith did an excellent summary about Converting Genome Coordinates From One Genome Version To Another but most of these tools actually need the "chain" file (that is the file that describes the pair-wise alignments between two genomes) so I would like to know how to create this file or whether there is any tool doing the coordinates transference just starting from the 2 genomes and a file of annotated features (eg bed, gff). Thanks!

alignment liftover coordinates assembly genome • 773 views

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modified 14 months ago by jean.elbers • 1.4k • written 14 months ago by Gabriel • 30

14 months ago by

benformatics • 1.9k

ETH Zurich

benformatics • 1.9k wrote:

Please use the search function.

The above post (answered by Pierre Lindenbaum) will bring you to this link. Looking into it there is an automated script that will generate a chain file for you.

ADD COMMENT • link written 14 months ago by benformatics • 1.9k

This is outdated and difficult to get working, I don't recommend it. Instead, I'd recommend flo (https://github.com/wurmlab/flo) like @jean.elbers suggested. Just beware, it can be pretty CPU and memory intensive for big genomes, and takes quite a while.

ADD REPLY • link written 14 months ago by juliette • 20

The UCSC option provides a script that was relevant in 2018. That is a bit too recent for me to deem outdated... furthermore it's a single script.

ADD REPLY • link written 14 months ago by benformatics • 1.9k

Sorry, I meant the first page you linked is outdated: "This page is an interesting historical discussion and well worth the read. "
As for the script, I personally found it difficult to follow. I didn't manage to get it working, and a lot of stuff is hard-coded into the script. It's just honestly easier to use flo, but it's always good to give another option.

ADD REPLY • link written 14 months ago by juliette • 20

Yes! Exactly because of this I was asking again! Thanks juliette!

ADD REPLY • link written 14 months ago by Gabriel • 30

14 months ago by

jean.elbers • 1.4k

jean.elbers • 1.4k wrote:

In that post you mention, there is flo https://github.com/wurmlab/flo, which I recommend and can also liftover GFF files.

ADD COMMENT • link written 14 months ago by jean.elbers • 1.4k

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