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!
1 answer
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.
•
written
by
tiago211287
Log in to answer this question.
-
lncRNA and ncPEPs identification
written by atharvakarkare14 •
-
Long non Coding RNA databases for GSEA and ORA
written by Van9 •
-
long non coding RNAs annotation file
written by annaA •
-
Accurately identifying long non coding RNA from stranded total RNAseq(rRNA depleted)
written by m.sadman.sakib
-
Tool: DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
written by pkouxa •
-
non-coding RNAs target predictions
written by Leite
-
Long non-coding RNA database in mouse
written by mkulecka
-
Downloading data from ENCODE
written by engineer.khan •
-
Differential Expression based on Sequences from lncRNA
written by Joel TM
-
Rna Regulation Of Gene Transcription Database
written by Anthony Mathelier
