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carp reads in my bacterial small RNome

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?

rna-seq
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updated by colindaven colindaven • written by demoraesdiogo2017 • demoraesdiogo2017

2 answers

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

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written by GenoMax GenoMax

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

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written by colindaven colindaven

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