deleted genes (cre-flox) appears in RNAseq analysis

Question

[supreet0716]

Hi,

We have RNAseq data comparing two cell types (pop1 and pop2) from PTEN/P53 null mouse (cre-loxp) to wild-type mouse. In IGV, I can still see some reads mapping to deleted exons of P53 (exon 2-10) but none to deleted exon of PTEN (exon 5). Is that generally observed in RNAseq analysis?

PTEN: floxed for exon 5

P53: Floxed for exon 2-10

libraries: polyA primed non-stranded 125bp

Steps: -STAR/2.4.0d (2pass) -DESEQ2

Main parameters:Reference genome: GRCm38.p3.genome.fa / GTF file: gencode.vM4.annotation.gtf

Please see attached IGV plots and let me know if you have any questions

[supreet0716]

each population had 5 replicates