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Old 05-02-2013, 06:39 AM   #1
Location: US

Join Date: Jan 2013
Posts: 78
Default How to use Ensembl or Gencode annotation for cufflinks?

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:
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.
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