I've been always using assembly and gtf files from iGenomes. But now I wanna try using ensembl GRCm38, but iGenomes only has 37. So I need to build bowtie index from ensembl fasta files. There are different classes of fasta files on its ftp: ftp://ftp.ensembl.org/pub/release-71..._musculus/dna/
I'm wondering which files I should use to build the index.
As for the GTF files, could I use the one on its ftp directly?
Then for human, I wanna try Gencode, but still, I don't know what fasta files I should use to build bowtie index.
Thanks.
I'm wondering which files I should use to build the index.
As for the GTF files, could I use the one on its ftp directly?
Then for human, I wanna try Gencode, but still, I don't know what fasta files I should use to build bowtie index.
Thanks.