ANNOTATION in the config file

[GeorgeBGM]

If I only have GFF files from different species, should my format inside the contig comment file be as follows:

[ANNOTATION]
Genome = Species1.gff , Species2.gff , Species3.gff , Species4.gff

Besides, does the .hal file have to contain sequence information for species 1, species 2 and species 3. Thank you in advance for your answer.

[ph09]

Hi -

Can you please explain what inputs you would be using for the CAT run?

The config [ANNOTATION] field is used to assign the reference genome against which you would like to annotate your other species. Currently, CAT supports using only one reference.

The hal file will have to be made using all the species you would like to annotate against the reference and the reference as well.

Please let me know if you need any further clarification.

Thanks!

[GeorgeBGM]

Hi,
I am reproducing the pangenome annotation in the A draft human pangenome reference article, and I wonder if I can add several GFF files of closely related species into the cat-hprc.gencode38.auto somes.config file to gain better gene annotate (these related species do not appear in the HAL file). Besides，should the chromosome names in the GFF files used in contig be consistent with those in the HAL file.

uigi --module cat RunCat --hal=CHM13-f1g-90-mc-aug11.hal --ref genome=GRCh38 --workers=8 --config=cat-hprc.gencode38.auto somes.config --work-dir work-hprc-gencode38-chm13 --out-dir out hprc-gencode38-chm13 --local-scheduler --assembly-hub --maxCores
8 --binary-mode local > cat.hprc.gencode38.autosomes.chm13.log

[diekhans]

Using multiple reference annotations in a single CAT run is not implemented. It is something we would like for the future, however we don't know when anyone will have the time to implement it. You could do independent runs for each reference GFF and then reconcile the resulting annotations your self. Yes, the contig names have to match. George-du ***@***.***> writes:

…

Hi, I am reproducing the pangenome annotation in the **A draft human pangenome reference** article, and I wonder if I can add several GFF files of closely related species into the **cat-hprc.gencode38.auto somes.config** file to gain better gene annotate (these related species do not appear in the HAL file). Besides，should the chromosome names in the GFF files used in contig be consistent with those in the HAL file. uigi --module cat RunCat --hal=CHM13-f1g-90-mc-aug11.hal --ref genome=GRCh38 --workers=8 --config=**cat-hprc.gencode38.auto somes.config** --work-dir work-hprc-gencode38-chm13 --out-dir out hprc-gencode38-chm13 --local-scheduler --assembly-hub --maxCores 8 --binary-mode local > cat.hprc.gencode38.autosomes.chm13.log