I am new to Trinity and galaxy instance (https://usegalaxy.org/). I have 17 samples pair ended. I was wondering if I have to use trimmomatic or fastq quality trimmer before I concatenate left-reads and right-reads, and then execute trinity. Thanks, Nihar
Doing QA/QC on your fastq data is a good idea. This tutorial explains the basics: https://galaxyproject.org/tutorials/ngs/#fastq-manipulation-and-quality-control. It is from the NGS Logistics tutorial listed at the Learning hub here: https://galaxyproject.org/learn/. Other tutorials have assembly help/method that you can also review.
And here are some quick guidelines for Trinity:
The forward and reverse reads should be in two distinct datasets when using the tool. The tool form in Galaxy will guide you if the paired-end option is selected.
The same exact sequences, in the same order, should be in both datasets. Doing QA can sometimes disrupt this content. Using the tools FASTQ interlacer will produce output with matched pairs (interlaced) and unmatched pairs (two outputs, not interlaced). Use the de-interlace tool on the matched pairs to create your fastq data inputs for Trinity.
Thanks, Jen, Galaxy
Jen, Thank you very much. I have 4 experimental conditions with each have 2-3 replicates and my goal is to characterize differential expression and gene quantification. So I was wondering if I should group my data sets according to the experimental conditions and then run QA/QC?!?! I am just making if I am do it right. So from your instructions "The forward and reverse reads should be in two distinct datasets when using the tool", I guess I do not need to group them. thank you for the tutorials, I will go through them. Regards, Nihar