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.
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Question: Tophat2 error when using a custom reference genome
10 months ago by
bisht20diksha • 10
bisht20diksha • 10 wrote:
ADD COMMENT • link •modified 10 months ago • written 10 months ago by bisht20diksha • 10
10 months ago by
Jennifer Hillman Jackson ♦ 25k
Jennifer Hillman Jackson ♦ 25k wrote:
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 COMMENT • link modified 10 months ago • written 10 months ago by Jennifer Hillman Jackson ♦ 25k
Update: Your custom genome contains IUPAC characters. This is what probably caused the indexing problem with Tophat/Bowtie.
ADD REPLY • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k
ohh..!! HISAT2 can also be used for spliced mapping, i didn't know that. Thank you for the info, ma'am.
ADD REPLY • link written 10 months ago by bisht20diksha • 10
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hi-this is to inform that STAR has started to work from this evening. And thanks for your anticipation.
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
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.
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.