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Exon-centric annotation files for MISO
I am using MISO to test for differential exon usage, and according to the manual of MISO here, the annotation files seem to be different depending on whether one wants to do an "exon-centric" or "isoform-centric" analysis. I have two questions:
1. The annotation file I am currently using is directly downloaded from Ensembl website (Homo Sapiens). This GTF file (or the GFF file) contains annotations for the "isoform-level", right?
2. In order to do exon-level inference, is there any tools available that can give me the output annotation file with (from MISO manual) the following features (i.e. work on the Ensembl GTF file):
an exon-centric annotation of an alternatively skipped exon would contain two isoforms, one containing the skipped exon and its two flanking exon, and another isoform containing only the two flanking exons. This “exon-centric” annotation does not incorporate other exons in the gene, and so Ψ values obtained from this annotation correspond only to the inclusion of the alternative exon relative to its two annotated flanking exons, without considering any other parts of the gene’s isoforms
Thanks a lot!
1. The annotation file I am currently using is directly downloaded from Ensembl website (Homo Sapiens). This GTF file (or the GFF file) contains annotations for the "isoform-level", right?
2. In order to do exon-level inference, is there any tools available that can give me the output annotation file with (from MISO manual) the following features (i.e. work on the Ensembl GTF file):
an exon-centric annotation of an alternatively skipped exon would contain two isoforms, one containing the skipped exon and its two flanking exon, and another isoform containing only the two flanking exons. This “exon-centric” annotation does not incorporate other exons in the gene, and so Ψ values obtained from this annotation correspond only to the inclusion of the alternative exon relative to its two annotated flanking exons, without considering any other parts of the gene’s isoforms
Thanks a lot!
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