Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Any One please provide protocol for Analysing long noncoding RNA illumina data in galaxy?
0
gravatar for shashikanth20
2.3 years ago by
shashikanth20 • 10
shashikanth20 • 10 wrote:

Hi every one i need assistance on accurate complete protocol on analyzing long non coding RNA illumina data in galaxy. starting from QC parameters to DE analysis

Thank you

noncodingrna • 568 views
ADD COMMENT • link •
modified 2.3 years ago by Mo Heydarian ♦ 830 • written 2.3 years ago by shashikanth20 • 10
1
gravatar for Mo Heydarian
2.3 years ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello,

There are quite a few published workflows available for RNAseq under Shared data --> Workflows on: useGalaxy.org.

Among these workflows is this reference based transcriptome profiling one (https://usegalaxy.org/u/biocrusoe/w/rnaseq-reference-based-by-nekrut) that has an extensive tutorial associated with it (https://github.com/nekrut/galaxy/wiki/Reference-based-RNA-seq).

You can import any of the published workflows to your personal Galaxy account and modify the parameters (and even the tools used) in the workflow editor.

After you have completed your differential expression analysis you can look specifically at your long non-coding RNAs. I would recommend using a reference transcriptome that has annotations for protein-coding and non-coding transcripts, such as Ensembl or RefSeq.

Cheers,

Mo Heydarian, Galaxy Team
ADD COMMENT • link written 2.3 years ago by Mo Heydarian ♦ 830
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour