# Latest **URL:** https://help.galaxyproject.org/latest.md?page=3 [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) **Page:** 4 --- ## [Paired Reads not all Paired](https://help.galaxyproject.org/t/paired-reads-not-all-paired/18152)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 17\ **Last updated:** [July 29, 2026, 1:57am UTC](https://help.galaxyproject.org/t/paired-reads-not-all-paired/18152 "2026-07-29T01:57:16Z")
I noticed an issue with some of my sequencing, I first noticed just looking at my forward and reverse reads, and saw that read numbers didn’t match on the forward and reverse. Some double checking and looking at my raw … --- ## [Bioconductor packages failing to install in Galaxy Europe Interactive R (cannot access repository index)](https://help.galaxyproject.org/t/bioconductor-packages-failing-to-install-in-galaxy-europe-interactive-r-cannot-access-repository-index/18086)
**Author:** [@noor\_ali](https://help.galaxyproject.org/u/noor_ali)\ **Replies:** 1\ **Last updated:** [July 28, 2026, 9:15pm UTC](https://help.galaxyproject.org/t/bioconductor-packages-failing-to-install-in-galaxy-europe-interactive-r-cannot-access-repository-index/18086 "2026-07-28T21:15:01Z")
Hello everyone, I am currently using the Galaxy Europe Interactive R environment for a single-cell RNA-seq analysis workflow, but I am running into a persistent issue when trying to install Bioconductor packages. Probl… --- ## [Download and Extract Reads in FASTQ help](https://help.galaxyproject.org/t/download-and-extract-reads-in-fastq-help/18091)
**Author:** [@Akshaya\_Marri](https://help.galaxyproject.org/u/Akshaya_Marri)\ **Replies:** 2\ **Last updated:** [June 21, 2026, 10:14am UTC](https://help.galaxyproject.org/t/download-and-extract-reads-in-fastq-help/18091 "2026-06-21T10:14:34Z")
unable to download file , not able to see file rig --- ## [How to manage the 267 GB for RNA seq analysis](https://help.galaxyproject.org/t/how-to-manage-the-267-gb-for-rna-seq-analysis/18089)
**Author:** [@Innocent\_Kwaku\_Dorvl](https://help.galaxyproject.org/u/Innocent_Kwaku_Dorvl)\ **Replies:** 3\ **Last updated:** [July 28, 2026, 9:06pm UTC](https://help.galaxyproject.org/t/how-to-manage-the-267-gb-for-rna-seq-analysis/18089 "2026-07-28T21:06:10Z")
Dear Galaxy Support Team, I am currently using Galaxy for RNA-seq analysis as part of a wheat rust resistance gene cloning project. My research involves EMS-induced susceptible mutants and resistant wild-type lines, and… --- ## [Is image correlation in GALAXY possible while preserving aspect ratio (no distortion only rotation/scaling)?](https://help.galaxyproject.org/t/is-image-correlation-in-galaxy-possible-while-preserving-aspect-ratio-no-distortion-only-rotation-scaling/18114)
**Author:** [@Norbert\_Feuerechse](https://help.galaxyproject.org/u/Norbert_Feuerechse)\ **Replies:** 1\ **Last updated:** [July 28, 2026, 9:00pm UTC](https://help.galaxyproject.org/t/is-image-correlation-in-galaxy-possible-while-preserving-aspect-ratio-no-distortion-only-rotation-scaling/18114 "2026-07-28T21:00:17Z")
Hello Galaxy team, I would like to perform image correlation in GALAXY EU while allowing translation, rotation, and uniform scaling, but preventing any aspect ratio distortion (i.e., no non-uniform scaling or shear). T… --- ## [Quota increase request for RNA-seq project](https://help.galaxyproject.org/t/quota-increase-request-for-rna-seq-project/18211)
**Author:** [@Sarah\_Aleid](https://help.galaxyproject.org/u/Sarah_Aleid)\ **Replies:** 1\ **Last updated:** [July 28, 2026, 8:42pm UTC](https://help.galaxyproject.org/t/quota-increase-request-for-rna-seq-project/18211 "2026-07-28T20:42:37Z")
My registered email is (admin redacted). The reason i need more storage is because I’m a mawhiba student and I’m doing a research, and i need more storage for data analysis to be able to continue my research. I need 250 … --- ## [Stringtie help related to GTF file for zebrafish genome](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210)
**Author:** [@poojashukla](https://help.galaxyproject.org/u/poojashukla)\ **Replies:** 2\ **Last updated:** [July 28, 2026, 8:30pm UTC](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210 "2026-07-28T20:30:55Z")
i want to know when i am doing stringtie and uploading GTF file of zebrafish genome its giving error or not matching notations with hisat2 in built genomic sequence, help me find zebrfish gemome GTF file that matches to … --- ## [Ribosomal Database Project and Greengenes Database for Metagenomic Analysis](https://help.galaxyproject.org/t/ribosomal-database-project-and-greengenes-database-for-metagenomic-analysis/18212)
**Author:** [@Vyenge\_Erre\_Gayosa](https://help.galaxyproject.org/u/Vyenge_Erre_Gayosa)\ **Replies:** 2\ **Last updated:** [July 28, 2026, 6:18pm UTC](https://help.galaxyproject.org/t/ribosomal-database-project-and-greengenes-database-for-metagenomic-analysis/18212 "2026-07-28T18:18:25Z")
Hello everyone, I am new to metagenomic analysis using Galaxy and would like to ask about reference databases for taxonomic classification. Is it possible to upload and use custom reference databases, such as the Ribos… --- ## [Do I need to redo PCA and UMAP if published cell type annotations are available?](https://help.galaxyproject.org/t/do-i-need-to-redo-pca-and-umap-if-published-cell-type-annotations-are-available/16929)
**Author:** [@artintz](https://help.galaxyproject.org/u/artintz)\ **Replies:** 4\ **Last updated:** [July 28, 2026, 11:47am UTC](https://help.galaxyproject.org/t/do-i-need-to-redo-pca-and-umap-if-published-cell-type-annotations-are-available/16929 "2026-07-28T11:47:27Z")
Hello there, I am working with a scRNA-seq dataset where the original publication already provides curated cell type annotations (in 3 levels in fact) in the metadata. My goal is to perform cell–cell communication analy… --- ## [I can't run EGSEA on DEGs generated by limma-voom](https://help.galaxyproject.org/t/i-cant-run-egsea-on-degs-generated-by-limma-voom/18213)
**Author:** [@bahar125d](https://help.galaxyproject.org/u/bahar125d)\ **Replies:** 1\ **Last updated:** [July 27, 2026, 11:27pm UTC](https://help.galaxyproject.org/t/i-cant-run-egsea-on-degs-generated-by-limma-voom/18213 "2026-07-27T23:27:25Z")
Hello, I am trying to run EGSEA un Galaxy. I already have my list of differentially expressed genes, run by Limma-Voom. I have 6 samples in total, 3 controls and 3 treated ones. According to the step-by-step tutorial on… --- ## [How to separate genomic from subgenomic RNA reads of Coronavirus?](https://help.galaxyproject.org/t/how-to-separate-genomic-from-subgenomic-rna-reads-of-coronavirus/18064)
**Author:** [@gi3547](https://help.galaxyproject.org/u/gi3547)\ **Replies:** 6\ **Last updated:** [July 27, 2026, 6:41pm UTC](https://help.galaxyproject.org/t/how-to-separate-genomic-from-subgenomic-rna-reads-of-coronavirus/18064 "2026-07-27T18:41:45Z")
Hello Everyone, I am a beginner Galaxy user, I sequenced total RNA of Coronavirus-infected huh-7 cells. First i filtered the human genome. Then mapped the rest of the reads. The problem is: there are reads belong to bot… --- ## [Action requires account activation error but no activation link was sent to email](https://help.galaxyproject.org/t/action-requires-account-activation-error-but-no-activation-link-was-sent-to-email/17731)
**Author:** [@jennielugw](https://help.galaxyproject.org/u/jennielugw)\ **Replies:** 12\ **Last updated:** [July 24, 2026, 8:10pm UTC](https://help.galaxyproject.org/t/action-requires-account-activation-error-but-no-activation-link-was-sent-to-email/17731 "2026-07-24T20:10:19Z")
--- ## [I don’t have the option to transfer files from an FTP server to my history on Galaxy.org](https://help.galaxyproject.org/t/i-don-t-have-the-option-to-transfer-files-from-an-ftp-server-to-my-history-on-galaxy-org/18176)
**Author:** [@Robert\_Rekawiecki](https://help.galaxyproject.org/u/Robert_Rekawiecki)\ **Replies:** 4\ **Last updated:** [July 21, 2026, 7:17am UTC](https://help.galaxyproject.org/t/i-don-t-have-the-option-to-transfer-files-from-an-ftp-server-to-my-history-on-galaxy-org/18176 "2026-07-21T07:17:11Z")
I don’t have the option to transfer files from an FTP server to my history on Galaxy.org. Unfortunately, Paste/Fetch Data isn’t working either and is displaying an error. I’m trying to transfer files directly from my com… --- ## [Increase FragPipe’s allocated memory](https://help.galaxyproject.org/t/increase-fragpipe-s-allocated-memory/18178)
**Author:** [@sxhao](https://help.galaxyproject.org/u/sxhao)\ **Replies:** 3\ **Last updated:** [July 20, 2026, 5:24pm UTC](https://help.galaxyproject.org/t/increase-fragpipe-s-allocated-memory/18178 "2026-07-20T17:24:51Z")
Hello, I am writing to ask whether it is possible to increase the memory allocation for FragPipe. I have around 3 million peptides. Even after reducing the number of samples and adjusting other parameters, I am still una… --- ## [lncRNA pipeline using GENCODE files](https://help.galaxyproject.org/t/lncrna-pipeline-using-gencode-files/18181)
**Author:** [@Ivan\_David\_Fonseca\_G](https://help.galaxyproject.org/u/Ivan_David_Fonseca_G)\ **Replies:** 2\ **Last updated:** [July 20, 2026, 4:27pm UTC](https://help.galaxyproject.org/t/lncrna-pipeline-using-gencode-files/18181 "2026-07-20T16:27:05Z")
Dear team, I’m seeking advice regarding an issue in my RNA‑seq analysis pipeline. My objective is to identify differentially expressed lncRNAs. The workflow I’m using includes fastp (trimming), HISAT2 (alignment), Strin… --- ## [Invocation ID in RO-Crate](https://help.galaxyproject.org/t/invocation-id-in-ro-crate/18190)
**Author:** [@LauLauThom](https://help.galaxyproject.org/u/LauLauThom)\ **Replies:** 0\ **Last updated:** [July 20, 2026, 3:07pm UTC](https://help.galaxyproject.org/t/invocation-id-in-ro-crate/18190 "2026-07-20T15:07:05Z")
Hi there, I am using the Workflow Run RO-Crate export feature of galaxy to ingest workflow invocations in our internal data-management system (LabID). I would like to also save the link to these invocations together wi… --- ## [Galaxy server/UI pagination bug](https://help.galaxyproject.org/t/galaxy-server-ui-pagination-bug/18175)
**Author:** [@12Benne](https://help.galaxyproject.org/u/12Benne)\ **Replies:** 5\ **Last updated:** [July 20, 2026, 3:02pm UTC](https://help.galaxyproject.org/t/galaxy-server-ui-pagination-bug/18175 "2026-07-20T15:02:23Z")
I’m encountering a non-tool specific bug with drop down lists. Tool collection selector loads only the 50 most recent eligible datasets. Running a job increases the count from 107 to 108, displays the new output, and re… --- ## [Cannot upload FASTQ files: "Action requires account activation" despite being logged in](https://help.galaxyproject.org/t/cannot-upload-fastq-files-action-requires-account-activation-despite-being-logged-in/18171)
**Author:** [@Michelle\_Theus](https://help.galaxyproject.org/u/Michelle_Theus)\ **Replies:** 1\ **Last updated:** [July 15, 2026, 8:48pm UTC](https://help.galaxyproject.org/t/cannot-upload-fastq-files-action-requires-account-activation-despite-being-logged-in/18171 "2026-07-15T20:48:56Z")
I’m using usegalaxy.org and signing in with my Google account (admin redacted). I can successfully log in, and my account appears to be active: Storage Dashboard shows 10.8 GB used of 268.4 GB (4%) I can access my Use… --- ## [Frozen Export History to File Source](https://help.galaxyproject.org/t/frozen-export-history-to-file-source/18168)
**Author:** [@LukaDM](https://help.galaxyproject.org/u/LukaDM)\ **Replies:** 1\ **Last updated:** [July 15, 2026, 7:42pm UTC](https://help.galaxyproject.org/t/frozen-export-history-to-file-source/18168 "2026-07-15T19:42:19Z")
Hello: I started exporting a 1.43 gb file using the tar.gz option with download link; it has been running for 5 hours. I would like to cancel it and re-start, but I don’t see that option. Do I have to just let it time-o… --- ## [I am unable to run tools and my previous data is erased from the history](https://help.galaxyproject.org/t/i-am-unable-to-run-tools-and-my-previous-data-is-erased-from-the-history/18156)
**Author:** [@Dhruvi\_Joshi](https://help.galaxyproject.org/u/Dhruvi_Joshi)\ **Replies:** 2\ **Last updated:** [July 14, 2026, 4:02pm UTC](https://help.galaxyproject.org/t/i-am-unable-to-run-tools-and-my-previous-data-is-erased-from-the-history/18156 "2026-07-14T16:02:31Z")
Hi. I have previously run data in galaxy. Now it’s all gone, and i am unable to run any new queries. How can I correct this --- ## [I'm encountering errors while running hicPCA analysis and need assistance](https://help.galaxyproject.org/t/im-encountering-errors-while-running-hicpca-analysis-and-need-assistance/18166)
**Author:** [@ahl](https://help.galaxyproject.org/u/ahl)\ **Replies:** 1\ **Last updated:** [July 14, 2026, 3:31pm UTC](https://help.galaxyproject.org/t/im-encountering-errors-while-running-hicpca-analysis-and-need-assistance/18166 "2026-07-14T15:31:26Z")
--- ## [Run Tool button is not working](https://help.galaxyproject.org/t/run-tool-button-is-not-working/18163)
**Author:** [@Doctor\_Geller](https://help.galaxyproject.org/u/Doctor_Geller)\ **Replies:** 9\ **Last updated:** [July 14, 2026, 2:05pm UTC](https://help.galaxyproject.org/t/run-tool-button-is-not-working/18163 "2026-07-14T14:05:58Z")
hi im using tool FALCO but when i click the button Run Tool its not working i dont get any respond or results. --- ## [GTDB-Tk Classify genomes error type 3](https://help.galaxyproject.org/t/gtdb-tk-classify-genomes-error-type-3/17736)
**Author:** [@Jesus\_Tapia](https://help.galaxyproject.org/u/Jesus_Tapia)\ **Replies:** 5\ **Last updated:** [July 13, 2026, 7:04pm UTC](https://help.galaxyproject.org/t/gtdb-tk-classify-genomes-error-type-3/17736 "2026-07-13T19:04:18Z")
error in GTDB-tk classifier usage: gtdbtk {de\_novo\_wf,classify\_wf,identify,align,infer,classify,root,decorate,infer\_ranks,ani\_rep,test,trim\_msa,remove\_labels,convert\_to\_itol,convert\_to\_species,export\_msa,c… --- ## [TGS-GapCloser Node mount error](https://help.galaxyproject.org/t/tgs-gapcloser-node-mount-error/18160)
**Author:** [@Rui\_Alves](https://help.galaxyproject.org/u/Rui_Alves)\ **Replies:** 2\ **Last updated:** [July 13, 2026, 6:44am UTC](https://help.galaxyproject.org/t/tgs-gapcloser-node-mount-error/18160 "2026-07-13T06:44:38Z")
Hi, I am using TGS-Gapcloser to try and close the gaps in an assembly, providing fasta for hifi long reads. I am using galaxy. It does not work. The error message is as follows: FATAL: While checking container encr… --- ## [ AMRFinderPlus database configuration error on Galaxy Europe](https://help.galaxyproject.org/t/amrfinderplus-database-configuration-error-on-galaxy-europe/18154)
**Author:** [@carmen.sanchez](https://help.galaxyproject.org/u/carmen.sanchez)\ **Replies:** 1\ **Last updated:** [July 12, 2026, 12:09pm UTC](https://help.galaxyproject.org/t/amrfinderplus-database-configuration-error-on-galaxy-europe/18154 "2026-07-12T12:09:48Z")
Subject: AMRFinderPlus database configuration error on Galaxy Europe Hello, I am using AMRFinderPlus on usegalaxy.eu with the AMRFinder database V4.2-2026-05-15.1. Every job fails before the analysis starts with the f… --- ## [Current implementation of GTDB-Tk Classify genomes is broken (wrong default arguments)](https://help.galaxyproject.org/t/current-implementation-of-gtdb-tk-classify-genomes-is-broken-wrong-default-arguments/18057)
**Author:** [@jvollme](https://help.galaxyproject.org/u/jvollme)\ **Replies:** 1\ **Last updated:** [July 12, 2026, 11:09am UTC](https://help.galaxyproject.org/t/current-implementation-of-gtdb-tk-classify-genomes-is-broken-wrong-default-arguments/18057 "2026-07-12T11:09:20Z")
It appears the current toolshed implementations version 2.7.1 and 2.7.2 on usegalaxy.eu are broken? It appears they are still trying to use the default argument “skip\_ani\_screen”, which however is deprecated since versio… --- ## [Errors during starting Galaxy on local server](https://help.galaxyproject.org/t/errors-during-starting-galaxy-on-local-server/18158)
**Author:** [@Charmax](https://help.galaxyproject.org/u/Charmax)\ **Replies:** 3\ **Last updated:** [July 10, 2026, 1:05pm UTC](https://help.galaxyproject.org/t/errors-during-starting-galaxy-on-local-server/18158 "2026-07-10T13:05:59Z")
I was trying to run galaxy on a server for around 1 week. However after I cloned the git repository and started “sh run.sh” directly, there were two error messages showing up: galaxy.tool\_util.toolbox.integrated\_panel… --- ## [Account activation required error on usegalaxy.org](https://help.galaxyproject.org/t/account-activation-required-error-on-usegalaxy-org/18125)
**Author:** [@Heba\_Hathout](https://help.galaxyproject.org/u/Heba_Hathout)\ **Replies:** 2\ **Last updated:** [July 10, 2026, 12:22am UTC](https://help.galaxyproject.org/t/account-activation-required-error-on-usegalaxy-org/18125 "2026-07-10T00:22:53Z")
Hello, I signed in with Google on usegalaxy dot org but I keep getting the message ’ Action requires account activation’ when trying to upload files. I never received an activation email. Please help activate my account,… --- ## [Mega Thread: Account activation email not received? How to get one!](https://help.galaxyproject.org/t/mega-thread-account-activation-email-not-received-how-to-get-one/18146)
**Author:** [@Andrea\_Leon](https://help.galaxyproject.org/u/Andrea_Leon)\ **Replies:** 2\ **Last updated:** [July 10, 2026, 12:15am UTC](https://help.galaxyproject.org/t/mega-thread-account-activation-email-not-received-how-to-get-one/18146 "2026-07-10T00:15:20Z")
Hello Galaxy Support Team, I am writing to request your help with my account activation. I created a new account on usegalaxy, but I have not received the activation email. I have already checked my Spam/Junk folders, a… --- ## [Can't upload history from galaxy.eu](https://help.galaxyproject.org/t/cant-upload-history-from-galaxy-eu/18115)
**Author:** [@Jon\_Colman](https://help.galaxyproject.org/u/Jon_Colman)\ **Replies:** 12\ **Last updated:** [July 9, 2026, 5:05am UTC](https://help.galaxyproject.org/t/cant-upload-history-from-galaxy-eu/18115 "2026-07-09T05:05:54Z")
Normally not a problem, though lately been extremely slow. Now all I get is an error when I try to upload to galaxy.org I tried copying link and pasting to galaxy.org, instant error. Tried copying history url and uploa… [Previous page](https://help.galaxyproject.org/latest.md?page=2) [Next page](https://help.galaxyproject.org/latest.md?page=4)