Question: Length of RNAseq reads
gravatar for silas008
3.4 years ago by
silas00880 wrote:


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?  


mirna rna-seq • 932 views
ADD COMMENTlink written 3.4 years ago by silas00880

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. 

ADD REPLYlink written 3.4 years ago by Sam2.3k

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. 

ADD REPLYlink written 3.4 years ago by Fabio Marroni2.2k
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