Dear all,
This question is somehow linked to my previous thread http://seqanswers.com/forums/showthread.php?t=49153 . I am analyzing RNA-Seq data from three breed groups (FIN, TEX, FXT) with two diet conditions (FLU, CON). The experimental design is attached below(expdesign.png). Two additional libraries were prepared for one sample each from three groups (FIN-FLU, TEX-FLU, FXT-FLU), and one library from FXT-CON group was sequenced three times. This is further explained by the second figure, where number of reads sequenced as well as percentage of mapped reads are different in former case but almost same in later case (ReadsMapped.png). Can I treat samples for first three groups as technical replicates? Or, given the fact that both the number of reads and the amount of reads mapped are almost same, can I just choose one sample from (37C5, 37C6, 37C7) and treat all samples in former case as just biological replicates? I would be grateful to get your feedback and suggestion. I am using DESeq2 for the differential expression analysis.
Thank you.
Keysoon
This question is somehow linked to my previous thread http://seqanswers.com/forums/showthread.php?t=49153 . I am analyzing RNA-Seq data from three breed groups (FIN, TEX, FXT) with two diet conditions (FLU, CON). The experimental design is attached below(expdesign.png). Two additional libraries were prepared for one sample each from three groups (FIN-FLU, TEX-FLU, FXT-FLU), and one library from FXT-CON group was sequenced three times. This is further explained by the second figure, where number of reads sequenced as well as percentage of mapped reads are different in former case but almost same in later case (ReadsMapped.png). Can I treat samples for first three groups as technical replicates? Or, given the fact that both the number of reads and the amount of reads mapped are almost same, can I just choose one sample from (37C5, 37C6, 37C7) and treat all samples in former case as just biological replicates? I would be grateful to get your feedback and suggestion. I am using DESeq2 for the differential expression analysis.
Thank you.
Keysoon
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