Recently, I obtained three RNA-seq pair-ended libraries for transcriptome assembly using trinity. The read number in total is nearly 290M while my server has a limited memory for 64G, which could not meet the requirement.
Could I do transcriptome assembly for each libraries and then merge them later somehow? Or other tools better than trinity in terms of memory usage efficiency?
Thank you!
HI Leavy,
Could you test the in silico Read Normalization?
It's an utility of Trinity.
Cris
Thanks for your advice, Cristina!
I read a comment about my issue here (http://ivory.idyll.org/blog/trinity-in-silico-normalize.html) and get a preliminary understanding about what you recommended to me and I indeed adopted that parameter during the running of Trinity. But I met another problem making Trinity broken with the words that "could not find libjava.so" and "Trinity cannot determine which version of Java is being used". Have you met this before?
Hi Leavy,
I recommend that you test that your Trinity installation is working using a much smaller subset of data. Follow the instructions on the Trinity website, and try running their test dataset. If you run into issues, then check their mailing list; I have solved many of my problems basically by copying the error message into a Google search and patiently reading through.
An alternative approach that might work better for you in the long run is to find a supercomputing resource with high memory nodes. That way, you can stop worrying about hardware limitations and dealing with configurations in your local machine.
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