Question: Tophat error: An error occurred with this dataset
gravatar for ravimore7
2.4 years ago by
ravimore70 wrote:


I am new to RNA-seq data analysis and want to identify differentially expressed genes from control and test samples mapping against Human (hg19) reference genome.

for this purpose, I am attempting to analyse AB SOLiD System 2.0 RNA-seq data with Galaxy.

I am running the pipeline as follows: (Tophat-Cufflinks-Cuffcompar-Cuffdiff).

step 1. I have converted RNA-seq data from AB SOLiD System 2.0 format to fastqsanger by using fastq groomer tool (with option Input FASTQ quality scores type Sanger & Illumina 1.8+)

However, when I run TopHat tool, I receive the following error:

An error occurred with this dataset: Fatal error: Tool execution failed

[2016-06-18 10:21:18] Beginning TopHat run (v2.0.14)

[2016-06-18 10:21:18] Checking for Bowtie Bowtie version: [2016-06-18 10:21:18] Checking for Bowtie inde

What is RNA-Seq analysis pipeline for data obtained from AB SOLiD System 2.0? What kind of steps I need to perform?

-Ravi More

rna-seq tophat • 812 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by ravimore70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour