Question: Rna-Seq With Reference Genome But No Gene Annotations
0
gravatar for Honey
5.9 years ago by
Honey200
Honey200 wrote:

I have an RNAseq data from a fungi and the public database for that particular fungi has whole genome shotgun sequences. But there are no gene annotations. Is it possible to analyze RNAseq data for differential expression by aligning to the shotgun reference genome.

Thanks

rnaseq seq • 2.5k views
ADD COMMENTlink modified 5.9 years ago by Nicolas Rosewick7.6k • written 5.9 years ago by Honey200
1
gravatar for Fabio Marroni
5.9 years ago by
Fabio Marroni2.2k
Italy
Fabio Marroni2.2k wrote:

Yes, for example you can use cufflinks to assemble trnascript without genome annotation: read the documentation here http://cufflinks.cbcb.umd.edu/

ADD COMMENTlink written 5.9 years ago by Fabio Marroni2.2k
1
gravatar for Nicolas Rosewick
5.9 years ago by
Belgium, Brussels
Nicolas Rosewick7.6k wrote:

On idea is to use a well annotated related species (in your case another fungi ) and to map the gene sequences ( use cDNA sequences, so UTR+exons ) with gmap ( it can output a gff file) to have an basic annotation.

ADD COMMENTlink written 5.9 years ago by Nicolas Rosewick7.6k
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