Question: Tophat2 error when using a custom reference genome
0
gravatar for bisht20diksha
5 months ago by
INDIA
bisht20diksha10 wrote:

why everytime tophat is showing error with the fastqsanger files ? "ERROR: An error occurred with this dataset." I am unable to understand this error, please help me with this.

ADD COMMENTlink modified 5 months ago • written 5 months ago by bisht20diksha10
1

hi-this is to inform that STAR has started to work from this evening. And thanks for your anticipation.

ADD REPLYlink written 5 months ago by bisht20diksha10

Hi - There seems to be a problem with the custom genome handling. Some tests are running, more feedback soon. Thanks for reporting the problem. Jen, Galaxy team

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k

The inputs look fine and the test rerun is still going. I ran the tool NormalizeFasta on the custom genome just to make sure the formatting was standardized. You might do this as well and then also rerun - it might resolve the indexing problem.

Your other option is to use HISAT2 instead. Tophat/Tophat2 are both considered deprecated and replaced by HISAT2.

More feedback once the test completes, likely later today or early tomorrow.

ADD REPLYlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k

thanks for the information ma'am. And yes HISAT2 can be used but i need splice aware mapper and HISAT is not a splice aware. I was also trying RNA-STAR but it is also not responding and showing error again and again.

ADD REPLYlink written 5 months ago by bisht20diksha10
2
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Ok, that's good, since it looks like the deprecated Tophat tool is not working with a custom genome right now. HISAT2 or RNA STAR are good alternatives. STAR does use much more memory during processing, so if your job fails for that reason, try HISAT2.

HISAT2 does do spliced mapping. See this tutorial for an example: https://galaxyproject.org/tutorials/nt_rnaseq/#spliced-mapping-with-hisat

All tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson25k
1

Update: Your custom genome contains IUPAC characters. This is what probably caused the indexing problem with Tophat/Bowtie.

ADD REPLYlink written 5 months ago by Jennifer Hillman Jackson25k

ohh..!! HISAT2 can also be used for spliced mapping, i didn't know that. Thank you for the info, ma'am.

ADD REPLYlink written 5 months ago by bisht20diksha10
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