Question: Non model organism(species) like planaria RNA SEQ analysis
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gravatar for hyojin0912
2.1 years ago by
hyojin09120
hyojin09120 wrote:

Hi

I'm analyzing planaria RNA seq for regeneration study

But planaria genome is not well organized(Use SmedGD v3.1 fasta & GTF)

So I do blastx to get uniprotID but I'm having over 2,000 species' uniprot ID

Also, I have an assigned GO to each gene then I want to analyze at GO level

Is there any tool or paper which I can see...

Last time, I done GO enrichment test using EASE test (DAVID software) but I don't have enough number of GO to each gene.. this is also a problem of my analysis

Please help me anything

I'm looking forward to your reply

Thanks

rna-seq • 532 views
ADD COMMENTlink written 2.1 years ago by hyojin09120

easiest thing you can do is to upload your blast results into BLAST2GO. It has everything you are asking for.

ADD REPLYlink written 2.1 years ago by ashish220

I already done B2G but blast ratio is too low..

ADD REPLYlink written 2.1 years ago by hyojin09120

you can try increasing the number of hits per query to consider but this would only work if you performed blastx using default parameters. If this doesn't help then then I think b2g cannot help you.

ADD REPLYlink written 2.1 years ago by ashish220
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