Hi, For some reason after alignment using STAR of my RNA-Seq reads and then feeding these files through the QoRTs package in UNIX I find that the majority of the graphs look similar, if not exact, to the QoRTs graphs generated from the pre-aligned files from Illumina. However, there was one graph which caught my eye as it had to do with chromosomal distribution and there appears to be something wrong?

For the graph I generated using my own aligned .bam files using STAR, the graph in question looks like this: https://prnt.sc/qtiizi

For the graph I generated using the already pre-aligned .bam files from Illumina, the graph in question looks like this: https://prnt.sc/qtiky6

My concern is that they should be exactly the same since it's coming from the same RNA-seq raw data. I'm just wondering if I should dwell on this too much as most of the other graphs look similar and I already had to feed my data through once before since I messed up the coding. It is very time-consuming and some people mention that they just outright skip this QC checkpoint.

What do you think?

Thanks, Yas