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

Hello,

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 • 897 views
ADD COMMENTlink modified 2.8 years ago by Chris Fields2.1k • written 2.8 years ago by nikelle.petrillo100
1
gravatar for Chris Fields
2.8 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 2.8 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 2.8 years ago by nikelle.petrillo100
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