Entering edit mode
8.0 years ago
nikelle.petrillo
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110
Hello all,
I am performing de novo transcriptome assembly on my paired end, illumina reads. I am going to create a transcriptome assembly using trinity, however, how do i go about concatenating my left and right reads? Do i need to merge together each left and right reads first and then somehow combine all of my samples? I am not familiar with the unix code that will do this.
Thanks for the help! Nikelle
Why are you looking to concatenate/merge your R1/R2 reads? No point in concatenating them and they can't be merged unless you know that the insert size will allow you to do so (i.e. sequencing length > insert size).
As Trinity page recommends this is all you need to do
Thank you,
So as Damian Kao said below me, should i be inputting all of my left reads into that trinity code, and then all of my right reads as well?
As @Damian pointed out in the example below make sure they are in the same order for
--leftand--right. It would also help if they have reads in same order (if you did any trimming then hopefully you used a PE aware trimmer) in each pair of files.By the way, Trinity will only use PE reads as extra information for bundling reads during the Chrysalis stage (unless something has changed in the newer versions that I am not aware of). It doesn't attempt do any scaffolding with them.
Thanks! And the code below, is it correct that there are no spaces before and after adding in a comma?
Nikelle