Hi,
I have RNAseq data with 1.5 M reads. But the general transcriptome coverge is very low. The percentage of gene covered over 70% at a given expression level is 20% only!
So I was thinking that for differential expression analysis I'll get low power because I've got a lot of gene with low coverage that may be false positive...
Do you think it could be a good idea to keep for differential analysis only gene with a moderate coverage like at least 50%??
When I do this I can found more differentially expressed gene! (7 instead of 2)
If someone has an opinion on this...
I have RNAseq data with 1.5 M reads. But the general transcriptome coverge is very low. The percentage of gene covered over 70% at a given expression level is 20% only!
So I was thinking that for differential expression analysis I'll get low power because I've got a lot of gene with low coverage that may be false positive...
Do you think it could be a good idea to keep for differential analysis only gene with a moderate coverage like at least 50%??
When I do this I can found more differentially expressed gene! (7 instead of 2)
If someone has an opinion on this...
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