Question: Create Chain File for Converting Genome Coordinates
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gravatar for Gabriel
14 months ago by
Gabriel30
Gabriel30 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!

ADD COMMENTlink modified 14 months ago by jean.elbers1.4k • written 14 months ago by Gabriel30
1
gravatar for benformatics
14 months ago by
benformatics1.9k
ETH Zurich
benformatics1.9k 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 COMMENTlink written 14 months ago by benformatics1.9k
1

This is outdated and difficult to get working, I don't recommend it.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 REPLYlink written 14 months ago by juliette20

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 That is a bit too recent for me to deem outdated...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 REPLYlink written 14 months ago by benformatics1.9k
1

Sorry, I meant the first page you linked is outdated: "This page is an interesting historical discussion and well worth the read.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 REPLYlink written 14 months ago by juliette20
1

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

ADD REPLYlink written 14 months ago by Gabriel30
1
gravatar for jean.elbers
14 months ago by
jean.elbers1.4k
jean.elbers1.4k wrote:

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

ADD COMMENTlink written 14 months ago by jean.elbers1.4k
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