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As you can see in the attached graph(#1), there are several genes that are unregulated in condition_1. But based on q-PCR I know that those genes (near the red arrow) are equally expressed in both conditions. If I do not allow the reads from highly down regulated genes (more than 2-fold) to be mapped to the genome (by replacing the sequence of highly down regulated genes with “N”s in the genome fasta file), I get the second graph which shows similar expression in both conditions for those genes.
Is the FPKM calculated correctly in the first graph?
Is there a way to fix this issue?
I have heard this is a common problem when lots of genes are down regulated in one condition.
I am analyzing unpaired RNA-Seq reads through Tophat, cufflink/cuffdiff pipeline.
Is the FPKM calculated correctly in the first graph?
Is there a way to fix this issue?
I have heard this is a common problem when lots of genes are down regulated in one condition.
I am analyzing unpaired RNA-Seq reads through Tophat, cufflink/cuffdiff pipeline.