Annotation file (gff3) for hg38 to be used with MISO

Question

[dina.hesham139]

Hey,

I'm using MISO for alternative splicing analysis, I mapped my samples against hg38 (ensembl). For those who are familiar with MISO, does anyone know how to obtain the annotation file needed -for hg38-?

Thanks in advance

Answer 1

[GenoMax]

GTF hg38 Ensembl.
GFF3 hg38 Ensembl.

[dina.hesham139]

Thank you aloooot :)

[subhabioc]

Will it work also for Tophat-Cufflink-Cuffdiff pipeline for RNA seq analysis? Did it work for you @dina?

[GenoMax]

Yes it should. Make sure you get the corresponding fasta (ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) to build your bowtie2 indexes from.