search

gagneurlab / MMSplice_MTSplice

Tissue-specific variant effect predictions on splicing
MIT License
39 stars 21 forks source link

Used in non-model species? #47

Closed FarmOmics closed 3 years ago

FarmOmics commented 3 years ago

As title shows, whether the software can be used in non-human species, such as pig, cattle, etc.?

s6juncheng commented 3 years ago

Hi Dailu,

We never tested our model for species other than human. I would assume there is some level of conservation in terms of splicing regulators across species. However, I would interpret the results with extra care.

You should still be able to run the software if you use standard file formats. The files required are the gtf file, the fasta file and the vcf file for variants. You could follow the README to run the model given the input files.

We also provides a colab notebook https://colab.research.google.com/drive/1Kw5rHMXaxXXsmE3WecxbXyGQJma80Eq6. Since the notebook was designed for human, if you chose to follow this notebook, be sure to substitute the files to your corresponding ones. Paticularly, for the line dl = SplicingVCFDataloader(genome_version, fasta, vcf), genome_version should instead be the file path to the gtf file.

Please do let me know if this works. I'm very happy to help.

Best, Jun