Question: do i need to run Trinity assembly ALL over?
gravatar for nikelle.petrillo
4.3 years ago by
Providence College, Providence, RI
nikelle.petrillo100 wrote:


I created a de novo transcriptome assembly using Trinity. The assembly took over two weeks to be completed.

I just noticed that one sample's reads that I had trimmed using Trimmomatic ended up being truncated. When I aligned these particular reads back to my assembly, there was a 0% alignment rate. I re trimmed the reads, and now that Trimmomatic seems to have worked properly, there is now an 80% alignment rate.

If possible, is there any way that I can somehow incorporate my re-trimmed reads into this already made assembly? I am very short on time and re-running a whole new assembly to include this newly, re-trimmed read is not possible right now.

Any help or insight would be very helpful, Nikelle

rna seq trininty assembly • 1.2k views
ADD COMMENTlink modified 4.3 years ago by Chris Fields2.1k • written 4.3 years ago by nikelle.petrillo100
gravatar for Chris Fields
4.3 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

Unfortunately I would say it's better to be safe than sorry and re-run the assembly. You can always normalize the data to help with the run time (though this only helps if you have tons >100M reads if I recall correctly).

ADD COMMENTlink written 4.3 years ago by Chris Fields2.1k

Thanks Chris, I had a feeling i would need to do this! Thanks for your feedback

ADD REPLYlink written 4.3 years ago by nikelle.petrillo100
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1282 users visited in the last hour