SNP or error in miRNA read?

[vebaev]

Hi,
I need advise since I'm not aware of SNPs area...

I observe 2 reads matching a mature miRNA which are most abundant ones:
1) first is perfect match with the mature with 200K counts
2) secong have 1 mismatch but have double read counts (400K) - more abundant than the perfect match!

I think this cannot be error since it is sequenced 400K times with the same mistmach? or I'm wrong?

Can I conclude that this can be SNP in the the miRNA or no?

Thanks

[eslondon]

There are several potential explanations for this type of resuts:

1)Post-transcriptional editing. This is a mechanism by which the actual microRNA sequence is edited after transcription. Initially it was thought to be very prevalent, but then later it was observed that often what is considered editing is actually a cross-mapping artifact.

2)Cross-mapping artifacts. Small RNAs such as micro-RNAs, Y RNAs and other small RNAs are often very similar to each other, with families of microRNAs sharing very similar sequence. Sometimes one base pair change is enough to switch from the sequence of a Y RNA to that of a micro-RNA.

These issues, as well as good additional references, are discussed in depth in this article:

http://genome.cshlp.org/content/20/2/257.full

So before jumping to conclusions you have to make sure that your 600K reads, once filtired for high quality base calls and mapped to the whole genome, are truly located in the best possible mapping location.

best regards

[vebaev]

Thanks eslondon,
I will look into that paper more deeply.