Question: HISAT2/TOPHAT alignment to a Rabbit Genome
gravatar for deemergd92
9 months ago by
deemergd920 wrote:

Hello, I have multiple samples of human stem-like cells that were retrieved from an animal model. I am getting low human alignment due to contamination between both species. When I aligned my data to the built-in rabbit genome under TopHat I got ~45% alignment. I am going through with all my samples and aligning to the built-in rabbit genome and I find that I keep getting an error "An error occurred setting the metadata for this dataset." ~~~ 0 lines recorded.

My question is: Why the error message for all my samples after the first sample went through fine but all the other replicates get this error? Also, I tried finding a FASTA rabbit genome to align to via HISAT2, but my genomes keep giving me error messages - anyone know a good link to rabbit_genome.fasta? I used HISAT2 to align all my samples to the human genome, but TOPHAT for rabbit due to the built in rabbit genome only being available in TOPHAT and my errors I receive for my rabbit genomes I manually upload.

Error Message

Any and all advice is appreciated! Cheers

tophat alignment rabbit hisat2 • 331 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by deemergd920
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The public Main Galaxy server at is presenting with job errors across many tools at this time. We are actively working to correct the issues.

Please follow this ticket for updates:

Once the server is corrected, retest your specific issue and comment here in your original post if the problems persist and we can troubleshoot the use case.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k

I'll hold tight. Thank you for the response!

ADD REPLYlink written 9 months ago by deemergd920
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