Question: motif detection from predicted gene models
0
gravatar for Kay
14 months ago by
Kay0
Liverpool, UK
Kay0 wrote:

I've got a genome sequence (in scaffolds), in fasta format, RNA-seq bam files, predicted gene models from Braker and Augustus, I was wondering how to predict motifs. How can I detect motifs, say in the highly expressed genes? I have been reading about MEME, Hommer, etc, does it matter if my genome is from parasites, not humans?

Do I have to use Chip-Seq data?

Thanks K

rna-seq motif • 418 views
ADD COMMENTlink modified 14 months ago by Carambakaracho1.2k • written 14 months ago by Kay0
0
gravatar for Carambakaracho
14 months ago by
Carambakaracho1.2k
Switzerland/Basel
Carambakaracho1.2k wrote:

Hi Kay,

there's many options, depending on the kind of motifs you're looking for

All of these tools should support non model organisms, though a bit caution is always required

ADD COMMENTlink written 14 months ago by Carambakaracho1.2k

thanks Carambakaracho, I will have a look, my concern is genes predicted braker or Augustus lack promoter/enhancer/silencer regions, these tools prict genes from the start codons till stop codons

ADD REPLYlink written 14 months ago by Kay0
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