Question: idenfying miRNA among my gene list
1
gravatar for F
2.6 years ago by
F3.4k
Iran
F3.4k wrote:

Hi,

via miRNA DE analysis in Candida albicans I extracted a gene list from cuffdiff, how I know which of them are miRNA??? I used DAVID for functional classification but there is no miRNA in the result

thank you in advance

mirna rna-seq • 798 views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 2.6 years ago by F3.4k
2

How did you obtain the data? RNA-seq? Or small-RNA-seq?

ADD REPLYlink written 2.6 years ago by WouterDeCoster38k
1

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by F3.4k
1

Did the GTF from ensemble contain miRNA annotation?

An alternative for ID conversion is biomart in ensembl.

ADD REPLYlink written 2.6 years ago by WouterDeCoster38k
1

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

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by F3.4k
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