I have two RNA-seq experiments. I first checked them to see whether they are single or pairedEnd using:
bamtools view -c -F 1 myfile.bam, bamtools view -c -f 1 myfile2.bam
There I saw that all reads are singleEnd. In the next step I uploaded my data in R, and counted the reads per feature by summarizeOverlaps.
x <- sumarizeOverlaps(features= myfeatures, reads= myrnaseq1, mode= IntersectionNotEmpty, singleEnd=T)
I repeated this with the second experiment. In the next step I performed a quality control to see how similar both experiments are: Basically by a dotplot in ggplot and adding a linear model (geom_smooth(method="lm")).. Surprisingly, the line was horizontal. However, after adding the argument ignore.strand=T, it works perfectly.
Do you have an explanation for that? Might there be problems with the protocol used to generate the data?