# How to use UMI-tools extract **URL:** \ **Category:** Uncategorized\ **Created:** [May 18, 2019, 3:56pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323 "2019-05-18T15:56:41Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 18, 2019, 3:56pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/1 "2019-05-18T15:56:41Z")
how to use **UMI-tools extract** in the galaxy web page window? ---
**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\ **Post date:** [May 18, 2019, 4:21pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/2 "2019-05-18T16:21:06Z")
Hi, upload your data to [usegalaxy.eu](http://usegalaxy.eu) and use this [tool](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/). Optionally, learn more about UMI processing here [https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna\_preprocessing/tutorial.html](https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/scrna_preprocessing/tutorial.html) and here [https://training.galaxyproject.org/training-material/topics/transcriptomics/](https://training.galaxyproject.org/training-material/topics/transcriptomics/). Hope that helps, Bjoern ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 18, 2019, 6:44pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/3 "2019-05-18T18:44:06Z")
Actually, I just can not find the path to use **UMI-tools extract**. I want to know click where I can use it? ---
**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\ **Post date:** [May 18, 2019, 6:56pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/4 "2019-05-18T18:56:04Z")
> I want to know click where I can use it? What does this mean? The tool is here: [Galaxy](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_extract/umi_tools_extract/) ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 18, 2019, 7:08pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/5 "2019-05-18T19:08:28Z")
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? ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 18, 2019, 7:15pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/6 "2019-05-18T19:15:49Z")
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. ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 18, 2019, 7:28pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/7 "2019-05-18T19:28:43Z")
What should I do, if l want to get the similar tool links like the web page your linked? ---
**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\ **Post date:** [May 18, 2019, 8:06pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/8 "2019-05-18T20:06:05Z")
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. ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 18, 2019, 9:47pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/9 "2019-05-18T21:47:40Z")
Yes, I am using it. Right now I figured out that if use [usegalaxy.org](http://usegalaxy.org) can not find UMI tool，if use [usegalaxy.eu](http://usegalaxy.eu) can find UMI tool easily. You can check it. ---
**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\ **Post date:** [May 19, 2019, 1:37pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/10 "2019-05-19T13:37:45Z")
@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 ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 19, 2019, 3:31pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/11 "2019-05-19T15:31:00Z")
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? ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 19, 2019, 3:44pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/12 "2019-05-19T15:44:44Z")
Even I did BAM to SAM the file work well. ---
**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\ **Post date:** [May 19, 2019, 3:55pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/13 "2019-05-19T15:55:43Z")
Can you submit a proper error report via the bug-button, this was I can look at it in more detail. ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 19, 2019, 9:14pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/14 "2019-05-19T21:14:34Z")
I already figure out the problem, thank you so much for helping me. ---
**Author:** ![webyoung](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/webyoung/32/536_2.png) [@webyoung](https://help.galaxyproject.org/u/webyoung)\ **Post date:** [May 20, 2019, 6:45pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/15 "2019-05-20T18:45:21Z")
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`? ---
**Author:** ![Gargi\_Mishra](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/gargi_mishra/32/947_2.png) [@Gargi\_Mishra](https://help.galaxyproject.org/u/Gargi_Mishra)\ **Post date:** [September 27, 2019, 9:42pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/16 "2019-09-27T21:42:07Z")
What is the alternative option of umi-tools at [use.galaxy.org](http://use.galaxy.org)? ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [October 1, 2019, 3:50pm UTC](https://help.galaxyproject.org/t/how-to-use-umi-tools-extract/1323/17 "2019-10-01T15:50:27Z")
Welcome @Gargi_Mishra Most single-cell analysis tools are not available at Galaxy Main [https://usegalaxy.org](https://usegalaxy.org). However, some, including `UMI-tools`, are hosted at Galaxy EU [https://usegalaxy.edu](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](http://usegalaxy.eu). > [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1): > > [Galaxy Training Network Tutorials](https://training.galaxyproject.org): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) and some are not. Where you can run each is noted per tutorial – click on the _Galaxy instances_ gear icon ![galaxyserversGTN](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1287f50cfcdaa1aad750fe323f96995260ac4947.png) to review the [Public Galaxy](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) training image, instructions for how to get it will be listed below the tutorial listings, per category.