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How did you obtain the data? RNA-seq? Or small-RNA-seq?
thank you data are from recently sequenced smallRNAs in C.albicans but because I did not find any unique miRNA GTF for this fungus in mirbase I used a GTF from ensemble. I extracted 400 significant DE gene by cuffdiff but I don't know how I find which of them are miRNAs and which the targets of miRNAs
Did the GTF from ensemble contain miRNA annotation?
An alternative for ID conversion is biomart in ensembl.
thank you
actually there was not any miRNAs in GTF which I used from ensembl ... but in gff3 I found many miRNAs but tophat2 terminated with error by gff3 ... I converted gff3 to GTF by cufflinks but the output was empty then finally I used GTF from ensembl although without any miRNA
the error by tophat2 was like this
[2016-09-09 23:15:08] Building transcriptome data files 111/tmp/CA
[FAILED]
Error: gtf_to_fasta returned an error.
anyway I run cuffdiff