# \#epigenetics **URL:** https://help.galaxyproject.org/tag/epigenetics/351.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Bismark mapping with Fatal Error exit](https://help.galaxyproject.org/t/bismark-mapping-with-fatal-error-exit/16390)
**Author:** [@pannareeb](https://help.galaxyproject.org/u/pannareeb)\ **Replies:** 2\ **Last updated:** [October 16, 2025, 7:00pm UTC](https://help.galaxyproject.org/t/bismark-mapping-with-fatal-error-exit/16390 "2025-10-16T19:00:42Z")
Hello Galaxy EU Admin, I am using Bismark Mapper for alignment of WGBS reads to Arabidopsis reference genome. I was working well for sample 1-5 (Fig 1), but for later samples (sample 6-8), it started to give an error wi… --- ## [Cut and run: MACS2 error](https://help.galaxyproject.org/t/cut-and-run-macs2-error/15808)
**Author:** [@bezinka](https://help.galaxyproject.org/u/bezinka)\ **Replies:** 6\ **Last updated:** [July 9, 2025, 12:39am UTC](https://help.galaxyproject.org/t/cut-and-run-macs2-error/15808 "2025-07-09T00:39:11Z")
Hi, I would like to ask for help with MACS2. I follow tutorial Epigenetics: CUT&RUN data analysis and I have problem with MACS2 tool. I tried to check: files are not empty, format of the file should be fine (I did singl… --- ## [Running nextflow nfcore pipelines using a singularity](https://help.galaxyproject.org/t/running-nextflow-nfcore-pipelines-using-a-singularity/7037)
**Author:** [@Ollie\_White](https://help.galaxyproject.org/u/Ollie_White)\ **Replies:** 6\ **Last updated:** [August 13, 2024, 2:20pm UTC](https://help.galaxyproject.org/t/running-nextflow-nfcore-pipelines-using-a-singularity/7037 "2024-08-13T14:20:51Z")
Hello, I was wondering if it is possible to run nextflow pipelines from nfcore on a locally installed galaxy server? See examples here Pipelines » nf-core The nextflow pipelines from nfcore are downloadable as singular… --- ## [Methlydacel methylation bias weird output - methylation almost 100% with strange spikes](https://help.galaxyproject.org/t/methlydacel-methylation-bias-weird-output-methylation-almost-100-with-strange-spikes/12715)
**Author:** [@Shanna](https://help.galaxyproject.org/u/Shanna)\ **Replies:** 2\ **Last updated:** [June 14, 2024, 7:30am UTC](https://help.galaxyproject.org/t/methlydacel-methylation-bias-weird-output-methylation-almost-100-with-strange-spikes/12715 "2024-06-14T07:30:20Z")
Hi all, I’m working on an RRBS methylation analysis pipeline and have run into an issue. I am using methyldackel to assess methylation bias. In most of the literature showing these methylation bias plots, the average m… --- ## [How to normalised ChIP-Seq data set with Spike-in](https://help.galaxyproject.org/t/how-to-normalised-chip-seq-data-set-with-spike-in/12622)
**Author:** [@moonmoondeb](https://help.galaxyproject.org/u/moonmoondeb)\ **Replies:** 1\ **Last updated:** [June 8, 2024, 1:05am UTC](https://help.galaxyproject.org/t/how-to-normalised-chip-seq-data-set-with-spike-in/12622 "2024-06-08T01:05:52Z")
Hi I am using ChIP-dataset with drosophila spike-in. But can not find out which tool I should use for the spike in normalization in Galaxy. Can you kindly help me. With regards Moonmoon --- ## [HiCexplorer issues](https://help.galaxyproject.org/t/hicexplorer-issues/12339)
**Author:** [@Millicen](https://help.galaxyproject.org/u/Millicen)\ **Replies:** 1\ **Last updated:** [April 29, 2024, 4:49pm UTC](https://help.galaxyproject.org/t/hicexplorer-issues/12339 "2024-04-29T16:49:55Z")
I am using Hi-C explorer to analyse my data with a custome reference genome. However, I am unable to generate an output with the hiCBuildMatrix. I keep getting errors despite several attempts --- ## [Troubleshooting Issue with hicBuildMatrix Tool for Analyzing HiC Data](https://help.galaxyproject.org/t/troubleshooting-issue-with-hicbuildmatrix-tool-for-analyzing-hic-data/11829)
**Author:** [@Sheng-Chieh\_Hsu](https://help.galaxyproject.org/u/Sheng-Chieh_Hsu)\ **Replies:** 1\ **Last updated:** [March 4, 2024, 9:59pm UTC](https://help.galaxyproject.org/t/troubleshooting-issue-with-hicbuildmatrix-tool-for-analyzing-hic-data/11829 "2024-03-04T21:59:34Z")
Hi, I attempted to analyze HiC data using hicBuildMatrix, but it seems that the tool isn’t functioning properly. It remains stuck in the “waiting to run” status indefinitely. Does anyone have a solution to this issue or … --- ## [hicBuildMatrix seeting for restriction cut file or a bin size](https://help.galaxyproject.org/t/hicbuildmatrix-seeting-for-restriction-cut-file-or-a-bin-size/11824)
**Author:** [@Sheng-Chieh\_Hsu](https://help.galaxyproject.org/u/Sheng-Chieh_Hsu)\ **Replies:** 1\ **Last updated:** [March 4, 2024, 9:45pm UTC](https://help.galaxyproject.org/t/hicbuildmatrix-seeting-for-restriction-cut-file-or-a-bin-size/11824 "2024-03-04T21:45:12Z")
Hello, I attempted to follow the tutorial (Hands-on: Hi-C analysis of Drosophila melanogaster cells using HiCExplorer / Epigenetics) for conducting HiC analysis. In the tutorial, it suggests selecting a “Bin size” for a… --- ## [ChIPseeker missing first peak in the interval file?](https://help.galaxyproject.org/t/chipseeker-missing-first-peak-in-the-interval-file/11210)
**Author:** [@Emilyet](https://help.galaxyproject.org/u/Emilyet)\ **Replies:** 2\ **Last updated:** [January 10, 2024, 5:35am UTC](https://help.galaxyproject.org/t/chipseeker-missing-first-peak-in-the-interval-file/11210 "2024-01-10T05:35:24Z")
I used MACS2 to call peak and obtained a narrow peak bed file with 30169 regions but after I input the sequence into chipseeker it shows it still have 30169 regions but when I view the interval file of annotation it has … --- ## [MACS on galaxy giving me an error with python: bad interpreter](https://help.galaxyproject.org/t/macs-on-galaxy-giving-me-an-error-with-python-bad-interpreter/8975)
**Author:** [@Roberto\_Ferrari](https://help.galaxyproject.org/u/Roberto_Ferrari)\ **Replies:** 0\ **Last updated:** [November 7, 2022, 9:50pm UTC](https://help.galaxyproject.org/t/macs-on-galaxy-giving-me-an-error-with-python-bad-interpreter/8975 "2022-11-07T21:50:33Z")
trying to run MACS peaks calling and getting this error: Messages from MACS: /bin/sh: /usr/local/tools/macs/1.3.7.1/devteam/package\_macs\_1\_3\_7\_1/a7ea583a35d2/bin/macs: /usr/local/python/2.7/bin/python: bad interpreter: … --- ## [The plotHeatmap (DeepTool) does not produce the desired heatmap/ ChIP-seq analysis (H3K4me3)](https://help.galaxyproject.org/t/the-plotheatmap-deeptool-does-not-produce-the-desired-heatmap-chip-seq-analysis-h3k4me3/11021)
**Author:** [@Manolis1](https://help.galaxyproject.org/u/Manolis1)\ **Replies:** 4\ **Last updated:** [October 27, 2023, 1:52pm UTC](https://help.galaxyproject.org/t/the-plotheatmap-deeptool-does-not-produce-the-desired-heatmap-chip-seq-analysis-h3k4me3/11021 "2023-10-27T13:52:05Z")
Hello, I am analyzing ChIP-seq data for identifying H3K4me3 epigenetic marks between a Wt and the deletion of my favorite methyltransferase. I have used for the mapping Bowtie2, for Peak calling MACS2 and for generating… --- ## [(HiCPlotTAD)This will generate an empty track!!](https://help.galaxyproject.org/t/hicplottad-this-will-generate-an-empty-track/10950)
**Author:** [@s10101282](https://help.galaxyproject.org/u/s10101282)\ **Replies:** 12\ **Last updated:** [October 21, 2023, 8:54pm UTC](https://help.galaxyproject.org/t/hicplottad-this-will-generate-an-empty-track/10950 "2023-10-21T20:54:01Z")
I am trying to plot TADs using the HiCPlotTADs tool in usegalaxy.eu, but I keep receiving the same error. INFO:pygenometracks.tracksClass:plotting 1. \[x-axis\] INFO:pygenometracks.tracksClass:plotting 2. \[hic matrix\] WAR… --- ## [Rfile throwing error](https://help.galaxyproject.org/t/rfile-throwing-error/11024)
**Author:** [@mehvi](https://help.galaxyproject.org/u/mehvi)\ **Replies:** 1\ **Last updated:** [October 20, 2023, 7:43pm UTC](https://help.galaxyproject.org/t/rfile-throwing-error/11024 "2023-10-20T19:43:07Z")
hi the r file generated as a result of peak calling using the macs2 file is having errors ? while reading the list its saying the next list name and throwing error Error: unexpected symbol in: "03173462,0.008282385763… --- ## [Usage help -- single end versus paired end BAM options](https://help.galaxyproject.org/t/usage-help-single-end-versus-paired-end-bam-options/10973)
**Author:** [@Heinrich\_Gompf](https://help.galaxyproject.org/u/Heinrich_Gompf)\ **Replies:** 4\ **Last updated:** [October 16, 2023, 5:28pm UTC](https://help.galaxyproject.org/t/usage-help-single-end-versus-paired-end-bam-options/10973 "2023-10-16T17:28:34Z")
I’m a very new user and so I’m following this video exactly (I have samples from two mice, so it’s even the same built-in genome as what’s used in the video, mm10): When I get to the featureCounts section … --- ## [What is the blue and red exactly in Plotheatmap after computeMatrix of my chip-seq bw files?](https://help.galaxyproject.org/t/what-is-the-blue-and-red-exactly-in-plotheatmap-after-computematrix-of-my-chip-seq-bw-files/10899)
**Author:** [@Emilyet](https://help.galaxyproject.org/u/Emilyet)\ **Replies:** 0\ **Last updated:** [October 5, 2023, 3:29pm UTC](https://help.galaxyproject.org/t/what-is-the-blue-and-red-exactly-in-plotheatmap-after-computematrix-of-my-chip-seq-bw-files/10899 "2023-10-05T15:29:58Z")
After I input my bigwig files of my chip-seq and input data, choose the chip-binding targets as the region to be plotted and using reference-point for output, others are default parameter and also default parameter for p… --- ## [Help with making peaks MACS Chip-sequence analysis](https://help.galaxyproject.org/t/help-with-making-peaks-macs-chip-sequence-analysis/10886)
**Author:** [@michele\_palermo](https://help.galaxyproject.org/u/michele_palermo)\ **Replies:** 1\ **Last updated:** [October 2, 2023, 7:11pm UTC](https://help.galaxyproject.org/t/help-with-making-peaks-macs-chip-sequence-analysis/10886 "2023-10-02T19:11:18Z")
I am part of a Coursera class and the then-professor has now passed so I cannot ask questions. The sequence that he showed is no longer applicable. So the question is after running Bowtie2 on a data set. I am using the d… --- ## [How to convert fastq.gz to fastqsanger.gz](https://help.galaxyproject.org/t/how-to-convert-fastq-gz-to-fastqsanger-gz/10684)
**Author:** [@Sheng-Chieh\_Hsu](https://help.galaxyproject.org/u/Sheng-Chieh_Hsu)\ **Replies:** 4\ **Last updated:** [August 24, 2023, 5:54pm UTC](https://help.galaxyproject.org/t/how-to-convert-fastq-gz-to-fastqsanger-gz/10684 "2023-08-24T17:54:25Z")
Hi, I’m attempting to analyze my ChIP-seq data in UseGalaxy. The data is in fastq.gz format and was generated by the NextSeq 2000. I’m aware that most tools in UseGalaxy require the fastqsanger format, so I’m trying to … --- ## [Metilene tool fails on ENCODE bigWigToBedGraph converted data](https://help.galaxyproject.org/t/metilene-tool-fails-on-encode-bigwigtobedgraph-converted-data/9723)
**Author:** [@qcsciphi](https://help.galaxyproject.org/u/qcsciphi)\ **Replies:** 15\ **Last updated:** [June 23, 2023, 8:14pm UTC](https://help.galaxyproject.org/t/metilene-tool-fails-on-encode-bigwigtobedgraph-converted-data/9723 "2023-06-23T20:14:42Z")
Dear specialists, Would you please provide guidance on why Metilene fails despite that the data is BamSort’ed. The last column is “Percentage of reads that show methylation” from ENCODE bigWig data converterd to BedGra… --- ## [MethylDackel, GTN Tutorial Galaxies, and DNA Methylation](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510)
**Author:** [@ntillquist](https://help.galaxyproject.org/u/ntillquist)\ **Replies:** 9\ **Last updated:** [June 20, 2023, 7:01pm UTC](https://help.galaxyproject.org/t/methyldackel-gtn-tutorial-galaxies-and-dna-methylation/6510 "2023-06-20T19:01:24Z")
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 s… --- ## [Metilene tool usage](https://help.galaxyproject.org/t/metilene-tool-usage/8441)
**Author:** [@srinivasa\_abishek](https://help.galaxyproject.org/u/srinivasa_abishek)\ **Replies:** 6\ **Last updated:** [June 20, 2023, 6:54pm UTC](https://help.galaxyproject.org/t/metilene-tool-usage/8441 "2023-06-20T18:54:20Z")
Hello there! I am working with WGBS data and I want to extract the DMRs in a particular mutant. I used bwameth to align the sequencing data to mm10 genome. After that, I sorted the alignment file and used methyldackel … --- ## [Score column in narrowPeak file?](https://help.galaxyproject.org/t/score-column-in-narrowpeak-file/10035)
**Author:** [@alexbisias](https://help.galaxyproject.org/u/alexbisias)\ **Replies:** 2\ **Last updated:** [May 10, 2023, 2:28pm UTC](https://help.galaxyproject.org/t/score-column-in-narrowpeak-file/10035 "2023-05-10T14:28:53Z")
Hi, I’m trying to carry out a DiffBind operation with peak files (in bed format) generated elsewhere. When selecting my input files and parameters, the default setting for Score Column for a narrowPeak file is column num… --- ## [How to arrange samples for Diffbind analysis](https://help.galaxyproject.org/t/how-to-arrange-samples-for-diffbind-analysis/9966)
**Author:** [@Zhen\_Kai\_Ngian](https://help.galaxyproject.org/u/Zhen_Kai_Ngian)\ **Replies:** 6\ **Last updated:** [May 4, 2023, 1:24pm UTC](https://help.galaxyproject.org/t/how-to-arrange-samples-for-diffbind-analysis/9966 "2023-05-04T13:24:01Z")
Hello all, I am new to ChIPseq and I’m having problems with Diffbind analysis. My control (WT) and treated (3xTG) samples was not assigned properly for differential analysis. Under the replicate column, Diffbind calls WT… --- ## [FastQC analysis of ChIPseq sample](https://help.galaxyproject.org/t/fastqc-analysis-of-chipseq-sample/9969)
**Author:** [@Anand](https://help.galaxyproject.org/u/Anand)\ **Replies:** 1\ **Last updated:** [April 27, 2023, 9:22pm UTC](https://help.galaxyproject.org/t/fastqc-analysis-of-chipseq-sample/9969 "2023-04-27T21:22:14Z")
Dear All, I am new to galaxy server and trying to analyze the ChI-seq data files. I run FastQC analysis for chipped fastq file and found per base sequence content error and warning for per base sequence GC content … --- ## [Chip-seq biological replicates, multiple timepoints](https://help.galaxyproject.org/t/chip-seq-biological-replicates-multiple-timepoints/9655)
**Author:** [@dkomar](https://help.galaxyproject.org/u/dkomar)\ **Replies:** 1\ **Last updated:** [April 13, 2023, 11:19pm UTC](https://help.galaxyproject.org/t/chip-seq-biological-replicates-multiple-timepoints/9655 "2023-04-13T23:19:32Z")
Hi, So unfortunatelly our bioinfo guy is unavailable and I need to analyze my ChIP-seq data myself. I need some guidance for the analysis with multiple biological repeats and differential binding between the treatments. … --- ## [Help with Diffbind and multiple conditions](https://help.galaxyproject.org/t/help-with-diffbind-and-multiple-conditions/9803)
**Author:** [@os306](https://help.galaxyproject.org/u/os306)\ **Replies:** 1\ **Last updated:** [April 12, 2023, 8:33pm UTC](https://help.galaxyproject.org/t/help-with-diffbind-and-multiple-conditions/9803 "2023-04-12T20:33:03Z")
Hello, I am trying to use Diffbind to analyze by ChIP-Seq data. I am looking at one epigenetic mark, and have five different conditions (Control treatment, Drug 1, Drug 2, Drug 3, Drug 4) with 2 replicates per condition… --- ## [Bowtie2 mapping statistics](https://help.galaxyproject.org/t/bowtie2-mapping-statistics/9736)
**Author:** [@TIRTHANKAR\_BANDYOPAD](https://help.galaxyproject.org/u/TIRTHANKAR_BANDYOPAD)\ **Replies:** 1\ **Last updated:** [March 29, 2023, 7:47am UTC](https://help.galaxyproject.org/t/bowtie2-mapping-statistics/9736 "2023-03-29T07:47:46Z")
Hello. I am using bowtie2 for my ChIP-seq analysis but not seeing the “tool standard error” for most of my files, though I can see that the job is successfully performed. It is coming up as “empty”. Consequently, I am no… --- ## [Problems with my Bismark Mapper results](https://help.galaxyproject.org/t/problems-with-my-bismark-mapper-results/9435)
**Author:** [@Emm](https://help.galaxyproject.org/u/Emm)\ **Replies:** 1\ **Last updated:** [March 1, 2023, 9:23pm UTC](https://help.galaxyproject.org/t/problems-with-my-bismark-mapper-results/9435 "2023-03-01T21:23:43Z")
Hi ! First of all, I’m very sorry in advance because I don’t have a lot of knowledge in bioinformatics, it’s all new to me. If you have some easy-understanding documentations to suggest me, I’m all ear ! My problem is … --- ## [Can't find Bowtie version1 in the tool boxes](https://help.galaxyproject.org/t/cant-find-bowtie-version1-in-the-tool-boxes/8923)
**Author:** [@Sherry](https://help.galaxyproject.org/u/Sherry)\ **Replies:** 2\ **Last updated:** [October 31, 2022, 4:34pm UTC](https://help.galaxyproject.org/t/cant-find-bowtie-version1-in-the-tool-boxes/8923 "2022-10-31T16:34:38Z")
Can anyone tell me how to find “Map with Bowtie for Illumina” from the tools? I searched “Bowtie” in the tool search, I only got “Bowtie2” and no “Map with Bowtie for Illumina”. However according to what I learned, I ne… --- ## [new annotated bacterial genome](https://help.galaxyproject.org/t/new-annotated-bacterial-genome/8894)
**Author:** [@Luisa\_Nieto](https://help.galaxyproject.org/u/Luisa_Nieto)\ **Replies:** 3\ **Last updated:** [October 26, 2022, 8:39pm UTC](https://help.galaxyproject.org/t/new-annotated-bacterial-genome/8894 "2022-10-26T20:39:43Z")
How can I incorporate an annotated bacterial genome for RNA sequencing analysis using galaxy? --- ## [outMultimapperOrder in STAR alignment](https://help.galaxyproject.org/t/outmultimapperorder-in-star-alignment/8366)
**Author:** [@Lidong](https://help.galaxyproject.org/u/Lidong)\ **Replies:** 2\ **Last updated:** [September 23, 2022, 12:12am UTC](https://help.galaxyproject.org/t/outmultimapperorder-in-star-alignment/8366 "2022-09-23T00:12:54Z")
Dear Galaxy, This is the first time I have ever posted anything about bioinformatics. I have been a 100% wet guy in a small lab. I never touched linux… I have no workstation to work on anyway. But with Galaxy, I have be… [Next page](https://help.galaxyproject.org/tag/epigenetics/351.md?match_all_tags=true&page=1&tags%5B%5D=epigenetics)