HI everyone:
I knockdown one protein to be believed to influence Splicing by RNAi, and sequence treated sample (siRNA target protein) and mock (siRNA target luciferase) by RNA-seq.
My stratege is very straightforward, counting reads spanning a specific exon junction, large different counts between treat and mock could reflect different exon junction splicing efficiency or "expression level".
but My RT-PCR confirm is very frustrated, most of all my picked exon junction show no difference.
My question is can I use counts of mapping to exon junction to represent expression level?
I knockdown one protein to be believed to influence Splicing by RNAi, and sequence treated sample (siRNA target protein) and mock (siRNA target luciferase) by RNA-seq.
My stratege is very straightforward, counting reads spanning a specific exon junction, large different counts between treat and mock could reflect different exon junction splicing efficiency or "expression level".
but My RT-PCR confirm is very frustrated, most of all my picked exon junction show no difference.
My question is can I use counts of mapping to exon junction to represent expression level?