Adding zebrafish genome builds to HiSat and Star aligners

Hi Galaxy team,

I would like to use HiSat or Star for aligning Zebrafish RNAseq data. Under Reference Genome there is a note “If your genome of interest is not listed, contact the Galaxy team (–genomeDir)”. If this is not the right contact, kindly redirect me.

Thank you.

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@Lena_Ho on https://usegalaxy.eu we have installed the Zebrafish Genome. We try to harmonize all reference genomes in the near future.

Hope that helps!
Bjoern

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Thanks so much! That was fast!

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HI Bjoern, I still don’t see the option for Zebrafish as a built-in genome…

Perhaps this was addressed offline already, but I found the danRerN genomes in both tools at https://usegalaxy.eu now.

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Thank you! I am using main galaxy and overlooked that it’s on galaxy.eu

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Hi, there might be something obvious I’m missing, but hope you can help. The Zebrafish Genome isn’t available as a built-in option for HiSat2 or Star on Galaxy.org. Rather than opening an eu account, is there any chance you could add this in please? or can I switch/transfer my account to the eu? Thank you.

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Hi @S_B!

There is a project underway to synchronize the data indexes across all usegalaxy.* servers but that is still a work in progress.

For now, use https://usegalaxy.eu if your genome is there. It is probably too large to use as a custom genome effectively at https://usegalaxy.org.

You can have an account at both servers. The terms are one account per user per public Galaxy server. All accounts are distinct.

Datasets can be moved between servers. Copy link under disc icon from one server, paste into the Upload tool on the other.

Most histories can be moved as well – use the History export/import functions (can be done by URL, no need to download).

Workflows would need to be downloaded/uploaded but these are small files. Do this from the “Workflow” view.

Hope that helps!

I resorted to using galaxy.eu. But beware that trimmomatic does not work on galaxy.eu for reasons I could not figure out. So if you using that to trim, your data will have to do some intergalactic travel. Trim on main galaxy, port to galaxy.eu for Hisat2.

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@Lena_Ho Thanks for the feedback. I’ll give Trimmomatic a test there to see if I can reproduce the error.

That went quick. Individual paired-end or single-end inputs, with or without the adaptor clip, both ran successfully. Collection paired, compressed or uncompressed fastq, also ran successfully.

I did notice that there are two versions of the tool on the https://usegalaxy.eu server. I used:

Use: FASTQ Quality Control >> Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.36.5)

This older version should probably be avoided and might be what is causing problems. It is several revisions/changes/bugfixes behind the current version that works.

Avoid: FASTA/FASTQ > Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.32.3)

ping @hxr about the duplicated/outdated tool visible in tool panel at eu server

@Lena_Ho Thanks for reporting the issue, give the updated tool a try, and see if that works for you. Will save data :small_airplane:

H Jennifer

Thank you for this information and the tips on transferring to the EU server.

Best wishes

Suchu

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NOted! THanks Jennifer.

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