# MethylDackel, GTN Tutorial Galaxies, and DNA Methylation **URL:** \ **Category:** Uncategorized\ **Tags:** gtn-tutorial, mapping, galaxy-docker, visualization, epigenetics\ **Created:** [August 15, 2021, 11:30am UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510 "2021-08-15T11:30:22Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![ntillquist](https://avatars.discourse-cdn.com/v4/letter/n/c68b51/32.png) [@ntillquist](https://help.galaxyproject.org/u/ntillquist)\ **Post date:** [August 15, 2021, 11:30am UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/1 "2021-08-15T11:30:22Z")
I was following the tutorial “DNA Methylation data analysis” and the MethylDackel tool that it says to use for Methylation bias and metric extraction can not be found. I tried to download the tutorial’s workflow and it says it is missing tools from the toolshed. Is there anyway to still use that tool? I have all my files in BAM format from using the bwameth tool but without the next tool I am stuck ---
**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:** [August 17, 2021, 8:57pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/2 "2021-08-17T20:57:16Z")
Hi @ntillquist The tool may not be installed at the public Galaxy server you are working at currently. Or, you own Galaxy if that is where you are working. Try working at one of the servers (or the Docker instance, if available) listed for the tutorial under the pull-down menu “Available on these Galaxies”. **GTN Tutorial** [DNA Methylation data analysis](https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html) **GTN Topic: Epigenetics** [Galaxy Training!](https://training.galaxyproject.org/training-material/topics/epigenetics/) **Screenshot** with that menu expanded. **[UseGalaxy.eu](http://UseGalaxy.eu)** is one good choice as GTN tutorials are routinely tested there. This tutorial happens to also be associated with a pre-configured Docker image – navigate back up to the topic level to find the details if that interests you. ![screenshot-methylation-seq-gtn-galaxies-menu](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/ce057171380e62190f2cbce5d1de29583892d2a1.png) Hope that helps! ---
**Author:** ![akanksha\_bafna](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/akanksha_bafna/32/3987_2.png) [@akanksha\_bafna](https://help.galaxyproject.org/u/akanksha_bafna)\ **Post date:** [June 14, 2023, 7:51pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/3 "2023-06-14T19:51:54Z")
Hi @jennaj . I am trying to run this tutorial on use [galaxy.eu](http://galaxy.eu). In the “Hands-on: Methylation extraction with MethylDackel section” I cannot find the option to " \* Set the parameter `Extract fractional methylation (only) at each position. This is mutually exclusive with --counts, --logit, and --methylKit` to `Yes`." , as mentioned in the tutorial. Please suggest ---
**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:** [June 14, 2023, 9:57pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/4 "2023-06-14T21:57:53Z")
Hi @akanksha_bafna Try clicking to open the tool directly. That points to the EU server, and opens the version of the tool supported in the tutorial. Be sure to look under advanced options too for options. Let us know if that is not enough and can look closer. These tutorials were just updated so are current. ---
**Author:** ![akanksha\_bafna](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/akanksha_bafna/32/3987_2.png) [@akanksha\_bafna](https://help.galaxyproject.org/u/akanksha_bafna)\ **Post date:** [June 15, 2023, 10:51am UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/5 "2023-06-15T10:51:51Z")
Hi, @jennaj . I opened the tool from [usegalaxy.eu](http://usegalaxy.eu) server and executed a job. I looked in advanced options as well but could not find the specified function to set the parameter. ---
**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:** [June 15, 2023, 5:48pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/6 "2023-06-15T17:48:06Z")
Hi @akanksha_bafna The tool can be opened directly from the tutorial. That points to the specific version of the tool that matches the tutorial. Or, you can navigate using the version’s menu [Changing the tool version](https://training.galaxyproject.org/training-material/faqs/galaxy/tools_change_version.html) I’m explaining since you might need to do this across tutorials and tools, so is good to learn how 🙂 Give that a try and if still stuck, I’ll explain the steps with screenshots. ---
**Author:** ![akanksha\_bafna](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/akanksha_bafna/32/3987_2.png) [@akanksha\_bafna](https://help.galaxyproject.org/u/akanksha_bafna)\ **Post date:** [June 16, 2023, 2:55pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/7 "2023-06-16T14:55:02Z")
@jennaj . Indeed an older version of the tool , had the missing parameter as advanced settings that helped me . Another question based on the course tutorial : for compute matrix it uses imported file CpGislands.bed. As per my understanding, this is for human genome . I am using mm10 methylation datasets. Please could you help me where can I find the CpGislands. bed to carry out the plotProfile and differential methylation. ---
**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:** [June 16, 2023, 7:56pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/8 "2023-06-16T19:56:08Z")
> [@akanksha\_bafna](#): > > imported file CpGislands.bed UCSC [https://genome.ucsc.edu/](https://genome.ucsc.edu/) has a track for this data associated with mm10. See their Table Browser. You can go there first and check the box for output to Galaxy, or open it from within Galaxy with the tool **UCSC main**. ---
**Author:** ![akanksha\_bafna](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/akanksha_bafna/32/3987_2.png) [@akanksha\_bafna](https://help.galaxyproject.org/u/akanksha_bafna)\ **Post date:** [June 19, 2023, 8:36am UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/9 "2023-06-19T08:36:30Z")
Hi @jennaj Thanks . I will do that . I reckon in the tutorial at no point it is mentioned to import CpGislands.bed as input and can be confusing . Perhaps adding it as data to upload prior might be useful. On a separate note I checked the workflow and would just like to clarify few parameters. In the tutorial : **MethylDackel** tool with the following parameters: - Choose at the first option `Load reference genome from` `Local cache` and for `Using reference genome`the value `hg38`. - Select for the option `sorted_alignments.bam` the computed bam file of step 4 of the `bwameth` alignment. - Use for `What do you want to do?` the value `Determine the position-dependent methylation bias in the dataset, producing diagnostic SVG images`. - Set the parameters `By default, if only one read in a pair aligns (a singleton) then it's ignored.` and `By default, paired-end alignments with the properly-paired bit unset in the FLAG field are ignored. Note that the definition of concordant and discordant is based on your aligner settings.` to `Yes`. Should we change the default settings of the above mentioned parameters and set it to “yes”. ---
**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:** [June 20, 2023, 7:01pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510/10 "2023-06-20T19:01:24Z")
Hello @akanksha_bafna If your reads are paired-end, then choose the pair-end end option with this tool, too. The concordant alignments flag in the BAM will be important to avoid over counting. **SAMtools stats** can count those up, and **Filter BAM** can remove the excess reads if you want to reduce the BAM size for some reason (example: to reduce the load on downstream tools).