how many reads is enough in miRNA-seq

[anyone1985]

I want to do some miRNA-seq of mouse, how many reads from Hiseq is enough for my further research? 10M, 20M or 30M?

[vebaev]

I think 10M is more than ok even for human for a regular miRNA job?
They say 6M clean reads are more than ok.

[anyone1985]

OK, i see. what standard should i take for the enough of a miRNA job? Coverage? Number of Reads?

[volks]

number of usable reads, i would say.
i agree that ~10M is more than fine.

[anyone1985]

usable reads? clean reads?
clean reads: the reads passed the filter
usable reads: maybe the reads mapping to the genome or miRbase
i don't know wheather i am right.

[volks]

usable reads: the number of reads you end up using for miRNA profiling.
depending on contamination with other RNAs, adapter dimers, etc .. this might be significantly lower than the number of sequenced reads.

[anyone1985]

thanks. I think i know