Finding gff3 or gtf files for small non-coding RNA
Hi everyone, Does anyone know where to get gtf or gff3 files for these small RNAs: piRNA, intron-derived miRNA, endogenuous siRNA, linc-RNA, lnc-RNA, sno-RNA, snRNA.
I am especially interested in intron-derived miRNA and endogenuous siRNA.
I know RNACentral, but it only has fasta files. I checked Ensembl as well on the ftp server, but couldn't find them, as well as on GENCODE, lncipedia and MiTranscriptome.
A direct link would be much appriciated. Thanks in advance everyone
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y.gladbach •
1 answer
What is wrong with downloading gene annotation from GENCODE and creating intron-derived miRNA by yourself?
- Download GENCODE GTF
- dataset A <- Select intron coordinates
- dataset B <- Select miRNA coordinates
- intron-derived miRNA <- Overlap datasetA and datasetB
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Have you looked at the gencode Gene/Transcript Biotypes https://www.gencodegenes.org/gencode_biotypes.html
Do they have biotypes intron-derived miRNA or endogenous siRNA?
@PoGibas hmmm... looks like not!
This has been addressed in: GTF/GFF for non-coding RNA