How to profile non-coding sequencing based on NONCODE and RNAseq data

Question

[niu2rseq]

Hello everyone,

I have some RNAseq data from my model animals and I want to profile the long non-coding RNAs.

I found this database greatly useful: http://www.noncode.org/download.php

They provided a lot of resources for non-coding RNAs.

Can someone pointed me a possible pipeline how I can use with tophat+cufflink pipeline with these resources to profile lncRNAs? Thank you!

Answer 1

[tiago211287]

You can use the Salmon/Sailfish program: http://www.cs.cmu.edu/~ckingsf/software/sailfish/index.html

Instead of working with reads, the fundamental unit of transcript coverage in Sailfish is the k-mer.

You can provide your reads, the fasta file you want to look for, from the noncode and sailfish will do the rest.

Read the manual.