mapping reads to known miRNAs precursors

[DZhang]

vebaev,

a straightforward way to check is to look at the alignments in any genomics viewer. It will tell you exactly which base(s) are not perfectly aligned for these genes. I believe some people allow one mismatch to accommodate sequencing errors or SNPs.

[vebaev]

Dear all,
I'm trying to estimate the all reads count that are mapped to a specific precursor. I have done it my using bowtie with no mistmaches -v 0
But in some papers and tools I see that thay allowed 1 mistmache?! I compared the results in both way. Most of the counts are similar but for some miRNAs thay are doubled like in mir143 bellow:

with 1 mistmach mapping:
miR-143 - 4,697,060
miR-10b - 520,833

with 0 mistmach mapping:
mir-143 - 1,976,574
mir-10b - 501,099

So which is the right way? I thought it should be with 0 mistmaches since non specific tags can align when mistmaches occure but some people do it? And if I want to estimate diff.expression I should know which method is most relevant?

Thanks