Question: Annotation file (gff3) for hg38 to be used with MISO
0
gravatar for dina.hesham139
2.6 years ago by
Egypt
dina.hesham139100 wrote:

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

rna-seq • 1.5k views
ADD COMMENTlink modified 2.6 years ago by genomax58k • written 2.6 years ago by dina.hesham139100
1
gravatar for genomax
2.6 years ago by
genomax58k
United States
genomax58k wrote:

GTF hg38 Ensembl.
GFF3 hg38 Ensembl.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by genomax58k

Thank you aloooot :)

ADD REPLYlink written 2.6 years ago by dina.hesham139100

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

ADD REPLYlink written 2.5 years ago by subhabioc0

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.

ADD REPLYlink written 2.5 years ago by genomax58k
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