Question: How To Compare 2 Differential Expressed Transcripts From 2 Different De Novo Assembly?
2
gravatar for nbvasani
5.4 years ago by
nbvasani230
United States
nbvasani230 wrote:

Hi Fellows,

I have generated 2 de novo transcriptome assembly using Velvet/oases and Trinity. Differential expressed transcripts was generated from both assembly using edgeR. Now I want to compare Differential expressed transcripts from both assemblies, to see how many transcripts are similar in both assembly. Hoping you guys can help me out.

I would really appreciate your feedback.

Thanks in advance.

Naresh

ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by nbvasani230

So you've mapped the same datasets to two different assemblies? Are you trying to assess the quality of the assemblies somehow?

ADD REPLYlink written 5.4 years ago by Damian Kao15k

Yes, I have mapped same dataset to two different assemblies. No I am not trying to assess the quality of the assemblies. But at some point I would like to assess the quality of assemblies. Actually with one of the Differential expressed transcript list generated from velvet/oases, I already did manual annonation from NCBi website. So in order to save time and labor work, now I want to compare Differential expressed transcript list generated from trinity to list generated from velvet/Oases.

Thanks for your feedback.

Naresh

ADD REPLYlink written 5.4 years ago by nbvasani230

I see. So you really just want to map the annotations from one assembly to the other assembly somehow?

ADD REPLYlink written 5.4 years ago by Damian Kao15k

Yes Damian Kao.

ADD REPLYlink written 5.4 years ago by nbvasani230
1
gravatar for Charles Warden
5.4 years ago by
Charles Warden6.5k
Duarte, CA
Charles Warden6.5k wrote:

Maybe you want to try something like these programs (which look for differences in read distributions first). They seem like a very reasonable strategy, although I have to admit that I've had some trouble getting NIKS to work (although it might have been an issue with my specific data and/or the fact that I didn't try super hard):

RUFUS: http://bioinformatics.bc.edu/marthlab/wiki/index.php/Andrew_Farrell#RUFUS

NIKS: http://sourceforge.net/projects/niks/

NIKS paper: http://www.nature.com/nbt/journal/v31/n4/full/nbt.2515.html

Otherwise, I think you would have to BLAST/BLAT your assembled contigs against a common reference and try to map the corresponding contigs (which won't be trivial)

ADD COMMENTlink written 5.4 years ago by Charles Warden6.5k

Thanks Cwarden45 for your feedback.

Naresh

ADD REPLYlink written 5.4 years ago by nbvasani230
1
gravatar for nbvasani
5.4 years ago by
nbvasani230
United States
nbvasani230 wrote:

Hi Cwarden45,

I was able to solve this problem, with your help. First I blastn one of my DE gene list with reference annoted DE gene list. I got output from blastn in .xml format, which I opened in blast2go tool. In blast2go tool I was able to observe which gene were mapped to reference DE gene list.

Thank you so much.

Naresh

ADD COMMENTlink written 5.4 years ago by nbvasani230

Ok, thanks - I'm glad to hear that. My main concern was that the mapping wouldn't be one-to-one (especially with the Trinity transcripts, which can be pretty large). However, it looks like things worked out in your case!

ADD REPLYlink written 5.4 years ago by Charles Warden6.5k

Ya, you are right about large transcripts. In blast2go tool, it pick up first match out of 3 or 4 match based on evalue.

ADD REPLYlink written 5.4 years ago by nbvasani230

Hi nbvasani,

Currently I am doing some stuff similar to yours. I just want to know that if I performed de novo assembly of same data set using Velvet/Oases and Trinity, how can I check which assembly is the better one at the first glance ? Are they N50, maximum transcript length .etc. ? My aim at the moment is not yet going to do DE analysis, but to do a whole transcriptome assembly and annotation for reference of this new organism.

Thank you in advance for your suggestion!

Best regards,

Phuong.

ADD REPLYlink written 3.2 years ago by pbigbig190
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