In the edgeR analysis, I utilized "total exon reads" as the raw counts. I am wondering if this is fine or not.
Thanks for any comments!
Thanks for any comments!
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What is your biological question of interest ? -
I have two groups. Each group has two subgroups. Each subgroup has 8 replicates. I want to know the differential expression of genes within subgroup, between subgroup and among group.
Thanks!Comment
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You sum the reads in all exons for each gene. That's a good approach. Some experimental protocols also get a lot of intronic reads because many RNAs weren't processed. This avoids that problem. Although it's still possible that in your cell type, the spliced structure of some genes be unannotated and novel. But, counting in exons is the simplest method to use.Comment
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Thank you for the comments!Comment
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