Question: Cufflinks for microRNA annotation
gravatar for bibilong1111
5.5 years ago by
United States
bibilong11110 wrote:

Hello. Could anyone suggest me how can I do microRNA annotation and quantification using RNA-seq data? Can I use cufflinks for this purpose?

noncoding rna microrna rna-seq • 2.0k views
ADD COMMENTlink modified 5.5 years ago by jperezboza0 • written 5.5 years ago by bibilong11110

For microRNAs you don't need cufflinks. The precursor is normally less than 100nt in length and normal RNA-Seq reads should be longer. Assure that you clip the adapter of your reads correctly (since they are longer than the molecule of interest) and use a regular mapping algorithm (e.g. Bowtie, segemehl, BWA, STAR, etc.). Assure that you turn on the multiple mapping paramter, since small RNAs are known to have multiple copies in the genome. Without multiple mapping, all these multi-copy genes would be filtered out.

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by David Langenberger9.5k
gravatar for jperezboza
5.5 years ago by
jperezboza0 wrote:


I am currently working on miRNA NGS. I tried to use Cufflinks but it seems that it is set so that you will only get the "exon" reads. I am currently using annotation from UCSC and bedtools intersect to annotate my reads. Then using a simple bash script to count the reads/miR (or tRNA, piRNA....etc).


ADD COMMENTlink written 5.5 years ago by jperezboza0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1255 users visited in the last hour