do i need to run Trinity assembly ALL over?

Question

[nikelle.petrillo]

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

Answer 1

[Chris Fields]

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).

[nikelle.petrillo]

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