how to detect cross contamination of RNA-seq

Question

[331607579]

can any one tell me how to detect cross contamination of RNA-seq that samples are same species

[BioinfGuru]

It will be obvious once you map them to your reference genome....contamination will dramatically lower the % of mapped reads (<80%). Once that happens... take a random sample of read sequences and BLAST them to confirm.

[Devon Ryan]

Note the "samples are the same species" part. The alignment rate will probably be unaffected.

[BioinfGuru]

"read the question" strikes again :)

[331607579]

Thank you,

I think this won't be working, because our RNA-seq from tumor sample of different patients.

however, this real inspiration for me, may cross-contamination samples are more closely.

Best

Answer 1

[Devon Ryan]

PCA and look for outliers? If the samples are from the same treatment groups then there's likely no way to detect cross contamination.