Question: TopHat Build in genomes
gravatar for newyasso
2.6 years ago by
newyasso0 wrote:

Hello I'm new in using TopHat for RNAseq data analysis I'm trying to align fastq files that generated from wheat (Triticum aestivum) samples but unfortunately it is not listed as a choice in "reference genome" select panel. So dose any one has a solution to overcome this step? Thanks in advance

rna-seq tophat alignment galaxy • 915 views
ADD COMMENTlink modified 2.6 years ago by christophe.habib340 • written 2.6 years ago by newyasso0
gravatar for christophe.habib
2.6 years ago by
christophe.habib340 wrote:

Hello, are you on your own local instance ? In this case, you need to use the data manager to create genome references that will be used by Tophat. The data manager of bowtie2 allow you to make the genome available for TopHat. Hope this will help you.

ADD COMMENTlink written 2.6 years ago by christophe.habib340

Hello Christophe, many thanks for you but i'm using the public server

ADD REPLYlink written 2.6 years ago by yasser.morsy10

You can check the Use a built in reference genome or own from your history and set it to Use a genome from history. There you have to select the corresponding FASTA file of the Triticum aestivum reference genome, and then tophat will first index the genome and then run Tophat's alignment itself. Because of the extra step it's probably a bit slower.

ADD REPLYlink written 2.6 years ago by y.hoogstrate460

Using a Custom reference genome is the correct choice for now. How-to details:

The wheat genome is on our list of genomes to consider adding the future. Track progress here:

ADD REPLYlink written 2.6 years ago by Jennifer Hillman Jackson25k

Many thanks for you Jennifer but unfortunately after i uploaded my genome i faced another error which is Hello I'm which is Fatal error: Tool execution failed Building a LARGE index

[2016-04-16 14:12:28] Beginning TopHat run (v2.0.14) [2016-04-16 14:12:28] Checking for Bowtie Bowtie version: [2016-04-16 14:12:28] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (genome.*.bt2) please if you have any suggestion for solving this issue inform me. Thanks in advance

ADD REPLYlink written 2.6 years ago by yasser.morsy10
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