Dear Forum,
I am completely new to RNA-seq analysis so would be very appreciative of any advice regarding my query.
I have multiple RNA-seq samples from two closely related species, and would like to identify differentially expressed orthologous genes.
Is a correct approach to first identify orthologs between the two species using OrthoMCL, annotate those orthologs using (?), align all RNA-seq samples to the orthologs using bowtie2/tophat2, and assemble transcripts and identify differentially expressed transcripts using cufflinks and cuffdiff?
Thank you for your help and advice!
Kate
I am completely new to RNA-seq analysis so would be very appreciative of any advice regarding my query.
I have multiple RNA-seq samples from two closely related species, and would like to identify differentially expressed orthologous genes.
Is a correct approach to first identify orthologs between the two species using OrthoMCL, annotate those orthologs using (?), align all RNA-seq samples to the orthologs using bowtie2/tophat2, and assemble transcripts and identify differentially expressed transcripts using cufflinks and cuffdiff?
Thank you for your help and advice!
Kate
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