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-   -   Using Galaxy Trinity de novo assembly to look for predicted sequence (http://seqanswers.com/forums/showthread.php?t=85642)

fishseq 11-14-2018 07:07 AM

Using Galaxy Trinity de novo assembly to look for predicted sequence
 
Hello all,

I am very new to this kind of work and took the time to read through many wikis and methods articles to get to where I am now before coming here as I didn't want to seem too desperate or waste anyone's time yet here I am, so I thank you kindly for your help.

I know the methods I have used so far may not be perfect and opinion differs on which quality software to use and whatnot but I am just trying to do something as a proof of concept, nothing that needs to be perfect at all (right now).

My organism "X" of interest has not had its genome sequenced but has freely available RNAseq reads. I pulled these, used AfterQC for quality. I then used the Galaxy (trinity de novo assembly) tool to attempt assembly. The program I have been using to actually look at the files is UGene as it is free and available for Mac. All I am trying to do now is open up the file with UGene and try to see if a predicted mRNA fragment for a protein from an organism "Y", whose genome has been sequenced, matches up at all with any of the contigs I assembled. I feel as if I've tried every button on the NGS tools drop down and the BLAST search but I am definitely doing something wrong.

I didn't know 99% of any of those words a few months ago so I really appreciate your patience and kindness.


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