do i need to run Trinity assembly ALL over?
1
0
Entering edit mode
6.5 years ago

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

trininty assembly rna seq • 1.6k views
ADD COMMENT
1
Entering edit mode
6.5 years ago
Chris Fields ★ 2.2k

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1704 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6