Duplicated exons issue

[AngryMaciek]

Dear Authors,

I am using the official annotation from ENSEMBL but the exons are not unique:

grep ENSE00001957285 Homo_sapiens.GRCh38.87.gtf

(This GTF can be downloaded from the official site: ftp://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens/ )

Also, the conversion method which you provided does not work, I assume that this happens because the file is ENSEMBL annotation(?) Could you please let me know how should I run rnaseqc with this particular GTF version?

[agraubert]

Edit: The latest version of the collapsing script can handle ENSEMBL annotations. I have tested it to verify that it works with the specific gtf you mentioned.

Let me know if this resolves your issue

[AngryMaciek]

I have tested the python script together with RNA-SeQC 2.3.5 and it works fine, thank you very much!