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