carp reads in my bacterial small RNome

Question

[demoraesdiogo2017]

Hello

I have a few E. coli small RNome samples I tried to align with both E. coli genome and only with the non-coding E. coli RNAs. In both cases, I had a high percentage of unnaligned reads (~90%).

I blasted a few of them, and sometimes I got fragments of phage viruses, other E coli strains and, curiously, Cyprinus carpo hits (all of them with a query cover of 40-60%). I also noticed that many of them end with some variation of a long sequence of AAAGGGGGGG's, which does not seem to be the case of the ones that aligned. This happened for every sample.

Has anyone experienced something similar?

Answer 1

[GenoMax]

Those carp hits are not real. Which DB were you aligning to? Someone submitted bad sequences to NCBI (without doing proper clean up) is more than likely the cause.

See: https://dgg32.medium.com/carp-in-the-soil-1168818d2191

Answer 2

[colindaven]

The carp genome is a well known problem going back to 2014 I think. It should really be thrown out of the databases or a new version created.

http://grahametherington.blogspot.com/2014/09/why-you-should-qc-your-reads-and-your.html