Hello, I am analyzing total RNA-seq results and checking them in IGV.
I have noticed that the results from our experimental samples are different from the public data downloaded from GEO. The top 6 tracks are from our experimental samples, and all the tracks below the reference are from the public data.
What I am curious about is why there are small read counts between the exons in our data, but in the public data, which used the same cell line and the same drug treatment, there are none and the results are clean. At which stage do these differences arise? Should we consider the small read counts in our samples as noise?
Assuming all display parameters are equal.
It also looks like all peaks across the whole length of the image are higher in your dataset. Have you compared overall sequencing depth between the local/public data sets?
No, not yet.. I'll check that out. Thank you!!