Reference Annotation GTF that includes piRNAs?

Question

[theune]

Hello,

Is there a GTF file for mouse that includes pIRNAs for annotation of small RNAseq data. I am using StringTie for annotation of small RNA seq. Stringtie runs fine using Gencode mouse reference gtf but this does not include piRNAs, only miRNAs and other snRNAs. When I try to run stringtie using gtf files from piRNABank or piRBase, i get an error "could not find any valid reference transcripts".

Is there a gtf file like the one from gencode that includes piRNAs, or is there someway I can generate a file such as this?

[kalavattam]

Have you looked into piRNAdb? I believe there are other databases and sources of piRNA annotations too, e.g., link.

[theune]

Yes I've tried the gtf file thats available on piRNAdb but when when I run stringtie I get an error saying there are no valid transcripts in this gtf

[kalavattam]

My initial thought is to compare the formatting of the piRNAdb gtf to the GENCODE gtf, which you've had success with. Although this is a well-defined file format, there can be subtle differences between gtfs from different resources. Doing this check would answer the question, 'Do we get errors because StringTie is expecting the gtf to be a certain way?'

Alternatively or additionally, do you want a gtf that contains standard gene annotations in addition to piRNA annotations? If so, and if presumably there are only piRNA annotations in the piRNAdb gtf, then you should look into merging the GENCODE and piRNAdb gtfs (provided that formatting is consistent between the two; if not, you'll need to do some reformatting).