Top Hat deprecation--what should I use?

Heads up! This is a static archive of our support site. Please go to help.galaxyproject.org if you want to reach the Galaxy community. If you want to search this archive visit the Galaxy Hub search

Latest

Open

RNA-Seq

ChIP-Seq

SNP

Assembly

Forum

Home

Welcome to Galaxy Biostar! User support for Galaxy! about • faq • rss

Log In

Sign Up

Question: Top Hat deprecation--what should I use?

1

7 months ago by

sadequr.rahman • 10

sadequr.rahman • 10 wrote:

Dear All,

I am a novice to Galaxy and I was working through the RNA-seq tutorial.

At one stage the tutorial asks you to use TopHat but when I went to the RNAseq tools I found out that it says TopHat is now being deprecated. Should we be using RNAstar instead now? Is there a tutorial for RNAstar please? Or do you suggest I continue using TopHat gapped until I am more confident about what I am doing?

rna-seq tophat star mapping hisat2 • 273 views

ADD COMMENT • link •

modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by sadequr.rahman • 10

1

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

STAR and HISAT2 are both better choices.

HISAT2 replaces Tophat/Tophat2. STAR is used for specific reasons and uses much more resources (memory) to process data and if that tool's functions are not needed, HISAT2 is the choice.

Please see the RNA-seq Galaxy tutorials for example usage and workflows: https://galaxyproject.org/learn/. Start with these, but review the others near the top of the list for general usage, data prep, and to learn about functions such as Dataset Collections:

RNA-seq: Introduction - an introductory tutorial for transcriptome analysis. https://galaxyproject.org/tutorials/rb_rnaseq
RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example. https://galaxyproject.org/tutorials/nt_rnaseq

Thanks! Jen, Galaxy team

ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Please log in to add an answer.

Similar posts • Search »

RNA-seq Analysis after CuffDiff: Clustering, etc
Hello - I am very new to RNA-seq analysis and am trying to figure out my next steps. I ran Toph...
A tool is marked deprecated, should I use it?
Hi, im following a guide about how to analyse RNAseq data to do differential expression analysis....
Tophat is deprecated; use replacement mapper HISAT2
Hi, I cannot see tophat in RNA analysis tool please guide me who is the error and how should I re...
Adding tools to a Galaxy server - Public URLs versus Private local/cloud Galaxies
Dear all, I am new to DNA methylation analysis. I want to use Galaxy and I have seen some tutori...
Error In Tophat
I have ran Tophat v1.4.0 and it is marked red and has an error " long_spanning_reads". What does ...
Tophat error "long_spanning_reads"
Hello. I have ran Tophat for Illumina with groomed RNA-seq data and it is marked red and has an ...
RNA-seq analysis in Galaxy
I am doing RNA-seq analysis for several mouse samples and I encounter problems during differentia...
Annovar is returning a file with only headers
Hi I am trying to do some variant analysis. I have mapped the reads using hg19 as reference thr...
Error for TopHat
Hello, I could not use TopHat for RNA-seq. I received error messages writing server error many t...

Content

Help

About
FAQ

Access

RSS
Stats
API

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by Biostar version 16.09

Traffic: 176 users visited in the last hour