How to use UMI-tools extract

how to use UMI-tools extract in the galaxy web page window?

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Hi,

upload your data to usegalaxy.eu and use this tool. Optionally, learn more about UMI processing here https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna_preprocessing/tutorial.html and here https://training.galaxyproject.org/training-material/topics/transcriptomics/.

Hope that helps,
Bjoern

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Actually, I just can not find the path to use UMI-tools extract. I want to know click where I can use it?

I want to know click where I can use it?

What does this mean?
The tool is here: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/

Thank you so much for helping me. Yes through your link, I can find it, but I still can not find it by myself, I want to know the upper and down selection links are what?

Why in my own opening web page I can not find the link for using UMI tool, but through the link you attached I can find it easily.

What should I do, if l want to get the similar tool links like the web page your linked?

Are you sure your are on the same Galaxy server? You can find UMI tools under “FASTA/FASTQ” or simply by searching for “umi tools”. But you need to be on the correct Galaxy server.

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Yes, I am using it. Right now I figured out that if use usegalaxy.org can not find UMI tool,if use usegalaxy.eu can find UMI tool easily. You can check it.

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@webyoung this is normal. Galaxy is framework and every server can define the set of tools to support.
The usegalaxy.* once will align closer in regards of tools in the near future, but do not expect that all Galaxy server have the same tools installed.

Ciao,
Bjoern

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Now,I see. But I followed your steps on “Pre-processing of Single-Cell RNA Data”, after the step “Filtering the BAM File”, the results showed error said can not read BAM file. Actually, the BAM file is no problem, what is the reason?

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Even I did BAM to SAM the file work well.

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Can you submit a proper error report via the bug-button, this was I can look at it in more detail.

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I already figure out the problem, thank you so much for helping me.

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Right now, I can complete all the steps of the training “Pre-processing of Single-Cell RNA Data”, but when I try analysis my own data, there are 3 files of fastq.gz: index, R1, R2. I still do not know how to do it. And if R1 and R2 already loaded, how to them into the
Paired Collection?How can I get my own file like the file of celseq_barcodes.192.tabular?

What is the alternative option of umi-tools at use.galaxy.org?

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Welcome @Gargi_Mishra

Most single-cell analysis tools are not available at Galaxy Main https://usegalaxy.org. However, some, including UMI-tools, are hosted at Galaxy EU https://usegalaxy.edu and other public servers.

If interested, there are tutorials from the GTN that focus on single-cell analysis. Find these under the tutorial group “Transcriptomics”. Start with “Pre-processing of Single-Cell RNA Data” – includes UMI-tools and will run at usegalaxy.eu.