I understand that profits are a companies' priority, but in this case it compromised scientific integrity. Please be critical of these companies' pipelines and try to bring as much of it in-house as possible to prevent issues caused by cost-cutting and general carelessness.

Wasted money aside, the project would have been misdirected by bad data and the reads would have ended up in publication and on public data repositories. I wonder how widespread the issue is?

Confirmed with the sequencing company that they did not do a gDNA digest on the column…

Why is this particularly irksome? The lab I am collaborating with and who had already planned on doing RNAseq before my involvement is not bioinformatically inclined and would have missed these issues.

Screwy results, so I investigated the mapping pattern more closely and found high rates of reads not mapping to features i.e. genes (mean = 23%, 1s.d. = 17%. n=6).

Furthermore, checking the read mapping with samtools mpileup showed relatively high and uniform coverage in the intergenic regions.