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: 188.8.131.52 [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?