How do I create a BSGenome for Gallus gallus from ENSEMBL? #1864
pcantalupo
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Hello,
I'm using the Multiome vignette https://stuartlab.org/signac/articles/pbmc_multiomic.html to analyze my Multiome data from Chicken (Gallus gallus species). I obtained the Fasta and GTF file from ENSEMBL and used it for
cellranger-arc count
Fasta: https://ftp.ensembl.org/pub/release-111/fasta/gallus_gallus/dna/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.dna.toplevel.fa.gz
GTF: https://ftp.ensembl.org/pub/release-111/gtf/gallus_gallus/Gallus_gallus.bGalGal1.mat.broiler.GRCg7b.111.gtf.gz
I'm stuck on the step of
RegionStats(pbmc, genome = BSgenome.Hsapiens.UCSC.hg38)
since there isn't an ENSEMBL BSgenome for Gallus gallus. I'm not sure how to proceed since I don't have any experience building BSgenome packages and it seems quite difficult to do so. Is there an easier way? Thank youBeta Was this translation helpful? Give feedback.
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