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2 hours ago by

Hi there,

I am working on an RNA seq project with non model organisms, where I am hoping to discover the differential expression of a specific set of genes and/or sequence variants of the genes. I am having issue with my workflow though and find myself going in circles as I am not sure how to call the specific gene targets or sequences from my assembly.

Workflow so far:
1. FastQC
2. Trimmomatic
3. FastQC (to verify trimming)
4. Trinity
5. Quality assessment with BUSCO and other methods
6. Salmon (through Trinity) from here I plan on using DESeq2

Also I am using TransDecoder and Trinotate to annotate my assembly (with Blastp, Blastx, and Pfam)

Is there something I may be missing, overlooking, or simply just over-complicating? Is it possible to pull target genes from my assembly and blast them?

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snow49640



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