Question: Can't use Tophat on Galaxy.
0
gravatar for krishnakarthik.vemuri
3.4 years ago by
krishnakarthik.vemuri10 wrote:

Hi, 

I am having difficulty figuring out the Tophat tool on Galaxy. I was trying to use the Tophat tool to map fastq files that  I uploaded from EBI SRA. I am unable to run the Tophat, on it, since Tophat does not appear to be recognizing the file. I have tried to run Tophat on another fastq file from the RNA-Seq exercise of Galaxy: 

https://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise

This appears to be running fine. As far as I can tell, the only difference between the two files is that the fastq file from the exercise is formatted as fastqsanger, while I cannot see that on the file I uploaded. How can I work around this? Do I need to convert my files into a different format? If so, how can I do this? 

Thanks for all your help and advice.

Edit: I am editing to include that I am using the usegalaxy.org site.

 

ADD COMMENTlink modified 3.4 years ago by Martin Čech ♦♦ 4.8k • written 3.4 years ago by krishnakarthik.vemuri10
1
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The sequence data must in fastqsanger format and have that datatype assigned. How to do both is in the Galaxy wiki here:

Tool does not recognize dataset

Best, Jen, Galaxy team

ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k
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