Fasta file from Gencode

Question

[rob.costa1234]

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

https://ibb.co/SmfYqNz

[ATpoint]

Do you plan to do traditional alignment (e.g. hisat2 or bwa, bowtie2...) or is this RNA-seq and you want to use quantifiers such as salmon or kallisto?

Answer 1

[GenoMax]

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.