Length of RNAseq reads

Question

[silas008]

Hi,

I need to do the mapping of RNAseq reads on mouse genome reference to find the miRNAs count. My data contains reads length 20-50nt, but miRNAs has about 22nt, so I wanna map just reads about this length.

What is the best:

• To filter (extract of the data) just reads 22nt
• To cut reads bigger than 22nt to obtain just reads with this length?

Thanks

[Sam]

I suggest you to first perform adapter trimming as they are the most likely source of the additional length. As for read length filtering, a simple perl script or awk script can easily achieve what you would like to do.

[Fabio Marroni]

Actually, I would be more flexible about read length. Previous posts (How can I accurately identify miRNA sequences from small RNA seq results) suggest to keep reads between 18 and 30.