convert hsa miRBase gff3 into gtf

Question

[anna.coenenstass]

Hi I am trying to get the coordinates of human mature miRNAs, e.g. hsa-miR-1-3p, hsa-miR-1-5p, ect because I want to use it for HTseq counting so I can get counts specifically for the mature forms and not the pre-miRNAs, as they are typically annoted in ENSEMBLE.

I downloaded the hsa.gff3 from mirbase (http://www.mirbase.org/ftp.shtml) and then used sed to get rid of the precursor coordinates.

Unfortunately I need the file in gtf format not gff3 so I can merge it with the rest coordinates of other small RNAs that I obtained from ensemble.

I think it should be possible to do so with sed/awk but unfortunately my knowledge of these tools is not extensive and I would be so thankful for some help with this. Basically what I need is to convert this gff3 file:

chr1 miRBase miRNA 17409 17431 . - . ID=MIMAT0027618;Alias=MIMAT0027618;Name=hsa-miR-6859-5p;Derives_from=MI0022705

chr1 miRBase miRNA 17409 17431 . - . gene_id "miR-6859-5p"; transcript_id "MIMAT0027618";

Any help would be greatly appreciated, I don;t want to use just the galaxy gffread tool as it will not give me the gene ids as I need it for counting...Thank you so much!

Answer 1

[Saber HQ]

GenomeTools is going to be very useful for you. GenomeTools

It has an aoption to deal with gff3 files, validate them, and also convert them into gtf files. There is an option called "-retainids" which you may use to keep your ids too. Just install it and read the help/documentation file to get started:

gt -gff3 -help

[anna.coenenstass]

Thanks a lot for this Saber, I just downloaded and installed it, but I find it hard to use, as the documentation is sparse. I just downloaded and used make to build the library as in the installation instructions. Which path do I need to use in order to use gt? Are there any example somewhere on how to get started after installing?