Navigating De-Novo RNA data

[kevluv93]

Hey guys, I just finished a de-novo transcriptome assembly with Trinity and Trinotate. These programs produce individual fastq files that will have the transcriptome in one file, the abundance count in another file, gene ontology in another, etc...

I'm trying to find RNA sequences that we've identified in a previous experiment in these fastq files, but right now I'm stuck just opening them with notepad and using ctrl + f to find my sequences.

How do you guys navigate RNA data? What programs do you use to search for sequences in de-novo transcriptomes? Right now I have textfiles with all the sequences bunched up next to each other and I need to organize them.

Also, for anyone with experience with Trinity, with the outputs of Trinotate (gene ontology, abundance count, etc) is there a way I can incorporate these files into my transcriptome so I can find a sequence and have its abundance and ontology displayed next to it? Basically, I don't want to find a gene, then have to open up another file to find the abundance count, then another to find the signal peptide region, you get my point.

Thanks for the help guys!

[GenoMax]

You can use blat to align RNA sequences from the previous experiments against the transcriptome you have assembled.

You will need to have access to a unix/linux machine, which I assume you have since you have done trinity analysis already.

[kevluv93]

I'm actually using Windows. I can find a linux machine and run these programs, but I used Trinity through an XSEDE supercomputer that doesn't have a graphic user interface. If you could suggest things that work on Windows I would much appreciate it, but I'll definitely give blat a try.