Fasta file from Gencode
If I have to use gff3 file of gencode as gene model (gencode.v35.annotation.gff3.gz ) which Fasta file should be used for alignment from https://www.gencodegenes.org/human/ as summarized in image below
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GenoMax
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rob.costa1234
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rob.costa1234
1 answer
Primary assembly fasta is what you need. If you are interested in haplotypes etc then get this file instead. Differences are noted in the description column.
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