Hits attribute meaning

[lpantano]

This attribute tries to say how many times the read has been mapped and is present in the file. It is to give a quick idea of uniqueness.

do you think is useful?

[ThomasDesvignes]

I think it is. But as revealed by the miR199 example in the paper, we should make a call on how things should be reported because right now it seems to be up in the air:

"In this situation, one can set “Hits=3” and take a similar approach as above. Alternatively, because this isomiR perfectly matches each genomic location, it could be listed in a single line with the ‘Hits’ attribute set to ‘1’ and the ‘Parent’ attribute would be used to reflect the multiple possible origin by having the three reference names separated by a comma character."

=> One situation should be selected to be consistent in our analysis/approach.
=> I'd vote for the "Hits=3" because it hits three loci in the genome (and to me, the genome should always be the reference, not any annotation database)

[phillipeloher]

I'd vote for the "Hits=3" because it hits three loci in the genome (and to me, the genome should always be the reference, not any annotation database)

If we had to pick only one approach, that would be my vote as well. We have used the Hit=N approach so far and currently use the genome as the reference for the first few columns.