Identifying gene sequence in RNA-Seq data
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5 days ago
snow4964 ▴ 10

Hi all,

Sorry ahead of time, RNA-Seq and bioinformatics is something I am new at and still learning as I go. I am trying to compare the sequences of a single gene across different species using RNA-Seq data to identify (structural) variants or anything mutations in different species that may impact function. Thankfully there is already a reference CDS of the gene, on NCBI, that I am focusing on.

The issue I am encountering is that I do not know of the proper workflow or methodology to compare this one gene across multiple species. Ultimately I may be, and probably am, overthinking and overcomplicating the process. Is it as simple as using BLAST with the gene or my RNA-Seq data as a reference? Any advice or suggestions would be much appreciated.

Thank you!

sequence genomic rna-seq alignment • 137 views
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Never mind my plan going forward is to use mafft (through OrthoFinder) by adding the fasta of my gene of interest to my samples and then searching for it manually

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