# \#dataset **URL:** https://help.galaxyproject.org/tag/dataset/40.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Why collections?](https://help.galaxyproject.org/t/why-collections/16411)
**Author:** [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Replies:** 0\ **Last updated:** [October 21, 2025, 10:41pm UTC](https://help.galaxyproject.org/t/why-collections/16411 "2025-10-21T22:41:50Z")
Collections are one of the super-killer features of Galaxy! By Anton Nekrutenko October 21, 2025 --- ## [rnaSPADES --nanopore: Confirming data format and shape for an input area](https://help.galaxyproject.org/t/rnaspades-nanopore-confirming-data-format-and-shape-for-an-input-area/17331)
**Author:** [@ARW-UBT](https://help.galaxyproject.org/u/ARW-UBT)\ **Replies:** 2\ **Last updated:** [January 21, 2026, 10:59am UTC](https://help.galaxyproject.org/t/rnaspades-nanopore-confirming-data-format-and-shape-for-an-input-area/17331 "2026-01-21T10:59:11Z")
Hello, I am experiencing difficulties loading Nanopore reads to rnaSPADES via the “Additional read file” section. I was able to combine Illumina reads into a dataset of paired end reads, but the ONT fastq.gz file (outp… --- ## [Third Party Identities](https://help.galaxyproject.org/t/third-party-identities/13911)
**Author:** [@Amit\_Pande](https://help.galaxyproject.org/u/Amit_Pande)\ **Replies:** 1\ **Last updated:** [November 14, 2024, 2:26pm UTC](https://help.galaxyproject.org/t/third-party-identities/13911 "2024-11-14T14:26:39Z")
Dear Galaxy, I have single cell FASTQ data, and would like to connect the STARSOLO run with my google drive paid account. I tired Zenodo but it give access to 50 GB data in the free account, I have 70GB. Kindly let me … --- ## [ExomeDepth datasets](https://help.galaxyproject.org/t/exomedepth-datasets/12354)
**Author:** [@Ricardo\_Chinchilla](https://help.galaxyproject.org/u/Ricardo_Chinchilla)\ **Replies:** 3\ **Last updated:** [June 6, 2024, 12:11am UTC](https://help.galaxyproject.org/t/exomedepth-datasets/12354 "2024-06-06T00:11:19Z")
Why the tool doesn’t recognize the bam dataset, it puts me that it’s unavailable --- ## [accidently clicked on delete all hidden content](https://help.galaxyproject.org/t/accidently-clicked-on-delete-all-hidden-content/12334)
**Author:** [@dilara\_gngr](https://help.galaxyproject.org/u/dilara_gngr)\ **Replies:** 2\ **Last updated:** [April 29, 2024, 12:13am UTC](https://help.galaxyproject.org/t/accidently-clicked-on-delete-all-hidden-content/12334 "2024-04-29T00:13:18Z")
Hi, While I was doing cutadapt I accidently clicked on the delete all hidden content and I tried to take it back by undeleting it but it doesn’t work. My current job is not running it shows paused. How can I fix it? --- ## [Using the same datasets across different histories](https://help.galaxyproject.org/t/using-the-same-datasets-across-different-histories/11524)
**Author:** [@Ana\_Luiza\_Pereira](https://help.galaxyproject.org/u/Ana_Luiza_Pereira)\ **Replies:** 1\ **Last updated:** [January 18, 2024, 7:41pm UTC](https://help.galaxyproject.org/t/using-the-same-datasets-across-different-histories/11524 "2024-01-18T19:41:10Z")
Hi, guys. Is it possible to use a tool using data from different histories in Galaxy? I need to use Roary, but the GFF files are in different histories. If yes, how can I do that? Thank you for your attention. --- ## [Change name of dataset in collection](https://help.galaxyproject.org/t/change-name-of-dataset-in-collection/10264)
**Author:** [@mfaleevs](https://help.galaxyproject.org/u/mfaleevs)\ **Replies:** 2\ **Last updated:** [June 16, 2023, 10:55am UTC](https://help.galaxyproject.org/t/change-name-of-dataset-in-collection/10264 "2023-06-16T10:55:54Z")
I am trying to add different tags to my datasets which are in a collection (output of HISAT2). Whenever I follow the manual listed for adding tags to datasets in collection nothing gets added. I am starting to suspect th… --- ## [User does not have permission to use dataset - original data purged](https://help.galaxyproject.org/t/user-does-not-have-permission-to-use-dataset-original-data-purged/8936)
**Author:** [@Fizz](https://help.galaxyproject.org/u/Fizz)\ **Replies:** 1\ **Last updated:** [February 10, 2023, 9:01pm UTC](https://help.galaxyproject.org/t/user-does-not-have-permission-to-use-dataset-original-data-purged/8936 "2023-02-10T21:01:55Z")
I shared a history with a colleague and then purged it from my account since I had no space. Colleague gets error “User doesn’t have permission to use dataset”. I understand I should have given all permissions when shari… --- ## [Dataset Error Report](https://help.galaxyproject.org/t/dataset-error-report/9268)
**Author:** [@laura\_95](https://help.galaxyproject.org/u/laura_95)\ **Replies:** 1\ **Last updated:** [January 10, 2023, 11:28pm UTC](https://help.galaxyproject.org/t/dataset-error-report/9268 "2023-01-10T23:28:58Z")
Hi everyone, I can’t upload all of my .gff local data. Some dataset could not be read and it seems to occur accidentally. The error info is Dataset Error Report An error occurred while running the tool DATA\_FETCH. A… --- ## [FASTA Header Changes not shown in BLAST database](https://help.galaxyproject.org/t/fasta-header-changes-not-shown-in-blast-database/7549)
**Author:** [@R\_J](https://help.galaxyproject.org/u/R_J)\ **Replies:** 3\ **Last updated:** [February 23, 2022, 5:27pm UTC](https://help.galaxyproject.org/t/fasta-header-changes-not-shown-in-blast-database/7549 "2022-02-23T17:27:26Z")
Hello everyone, I used the “Text Transformation” tool in Galaxy to use the sed function to change the FASTA headers for my sequence files. When I convert these sequence files into a BLASTn database through the “makeblas… --- ## ["An error occurred setting metadata for this data set"-STR DETECTION](https://help.galaxyproject.org/t/an-error-occurred-setting-metadata-for-this-data-set-str-detection/7521)
**Author:** [@libinglin](https://help.galaxyproject.org/u/libinglin)\ **Replies:** 7\ **Last updated:** [February 18, 2022, 4:45am UTC](https://help.galaxyproject.org/t/an-error-occurred-setting-metadata-for-this-data-set-str-detection/7521 "2022-02-18T04:45:45Z")
I am getting error with the STR DETECTION. This file cannot be used for further analysis. /corral4/main/jobs/040/701/40701606/galaxy\_40701606.sh: line 123: galaxy-set-metadata: command not found --- ## [How to import a Dataset 'from User Directory'](https://help.galaxyproject.org/t/how-to-import-a-dataset-from-user-directory/7526)
**Author:** [@Jin](https://help.galaxyproject.org/u/Jin)\ **Replies:** 3\ **Last updated:** [February 16, 2022, 8:40am UTC](https://help.galaxyproject.org/t/how-to-import-a-dataset-from-user-directory/7526 "2022-02-16T08:40:47Z")
Hi, I’m trying to import a Dataset from User History In the Datasets dropdown list, from History item is visible but from User History does not show up for a non-admin user. For an admin of the Galaxy instance, from … --- ## [Datasets transfer from usegalaxy.org to usegalaxy.eu](https://help.galaxyproject.org/t/datasets-transfer-from-usegalaxy-org-to-usegalaxy-eu/6856)
**Author:** [@marcinschmidt](https://help.galaxyproject.org/u/marcinschmidt)\ **Replies:** 19\ **Last updated:** [October 19, 2021, 3:59pm UTC](https://help.galaxyproject.org/t/datasets-transfer-from-usegalaxy-org-to-usegalaxy-eu/6856 "2021-10-19T15:59:48Z")
I wanted to move/copy my dataset collection (fastqsanger.gz files, \>2GB each) from usegalaxyorg to usegalaxyeu as on the latter server there is a tool I am going to use. I tried to do as it was written in Question 2, Hel… --- ## [Help with datasets](https://help.galaxyproject.org/t/help-with-datasets/5553)
**Author:** [@HUJI\_stu](https://help.galaxyproject.org/u/HUJI_stu)\ **Replies:** 2\ **Last updated:** [August 17, 2021, 12:43pm UTC](https://help.galaxyproject.org/t/help-with-datasets/5553 "2021-08-17T12:43:37Z")
Hello, I have been use galaxy for the last couple of weeks in order to analyze RNA-seq. Today I logged in to my account and found out my History has been deleted and the datasets are are accessible only through User\>dat… --- ## [error join two data sets](https://help.galaxyproject.org/t/error-join-two-data-sets/5739)
**Author:** [@MariaGouli](https://help.galaxyproject.org/u/MariaGouli)\ **Replies:** 0\ **Last updated:** [April 3, 2021, 2:23pm UTC](https://help.galaxyproject.org/t/error-join-two-data-sets/5739 "2021-04-03T14:23:19Z")
Hallo, I started a coursera course on genomics and the first assignment is to work with datasets. I am joining two datasets and i am getting the error data file has frown too big showing is around 200 Gb after many hour… --- ## [built-in genome hg19](https://help.galaxyproject.org/t/built-in-genome-hg19/5673)
**Author:** [@roselucia](https://help.galaxyproject.org/u/roselucia)\ **Replies:** 1\ **Last updated:** [March 22, 2021, 10:42am UTC](https://help.galaxyproject.org/t/built-in-genome-hg19/5673 "2021-03-22T10:42:42Z")
Hi everyone, I used a built in Genome for bcftools norm on Galaxy EU server. Can I find more information about the built in genome (Human (Homo sapiens): hg19)? Which hg19 release is used for this built-in genome? Or do… --- ## [De novo analys still running](https://help.galaxyproject.org/t/de-novo-analys-still-running/5393)
**Author:** [@RinRyn](https://help.galaxyproject.org/u/RinRyn)\ **Replies:** 2\ **Last updated:** [February 17, 2021, 7:03pm UTC](https://help.galaxyproject.org/t/de-novo-analys-still-running/5393 "2021-02-17T19:03:44Z")
i start run de no vo (trinity) analysis last Tuesday, it still running. does it something wrong? --- ## [Downloading data](https://help.galaxyproject.org/t/downloading-data/3238)
**Author:** [@lambard\_alexandre](https://help.galaxyproject.org/u/lambard_alexandre)\ **Replies:** 9\ **Last updated:** [May 15, 2020, 7:23am UTC](https://help.galaxyproject.org/t/downloading-data/3238 "2020-05-15T07:23:01Z")
hello i runned kind off 20 jobs that ended but i cant download the results as a file , anyone could know why so ? --- ## [Galaxy API "GET" query: error message and troubleshooting](https://help.galaxyproject.org/t/galaxy-api-get-query-error-message-and-troubleshooting/2532)
**Author:** [@kkech](https://help.galaxyproject.org/u/kkech)\ **Replies:** 3\ **Last updated:** [November 26, 2019, 3:19pm UTC](https://help.galaxyproject.org/t/galaxy-api-get-query-error-message-and-troubleshooting/2532 "2019-11-26T15:19:36Z")
Hi, I have a problem getting the error message from the galaxy. I am using histories/{historyId}/contents/{contentId}, but when I get the error message(misc info field of JSON), the message is cropped. Do you know why … --- ## [file name restrictions](https://help.galaxyproject.org/t/file-name-restrictions/2494)
**Author:** [@blainedeyoung](https://help.galaxyproject.org/u/blainedeyoung)\ **Replies:** 4\ **Last updated:** [November 20, 2019, 3:23pm UTC](https://help.galaxyproject.org/t/file-name-restrictions/2494 "2019-11-20T15:23:49Z")
Do you have a list of characters not allowed in file names? Is there a maximum length on file names? --- ## [\[Solved\] Get datasets from docker mapping directory](https://help.galaxyproject.org/t/solved-get-datasets-from-docker-mapping-directory/1714)
**Author:** [@i-guigon](https://help.galaxyproject.org/u/i-guigon)\ **Replies:** 7\ **Last updated:** [July 16, 2019, 3:05pm UTC](https://help.galaxyproject.org/t/solved-get-datasets-from-docker-mapping-directory/1714 "2019-07-16T15:05:36Z")
Hello everyone. A few months ago I created for a colleague of mine a Galaxy instance using Docker on a virtual machine on our cloud. After she was done with her analyses and I explained her how to download her results,… --- ## [Downloading large files](https://help.galaxyproject.org/t/downloading-large-files/1717)
**Author:** [@Michael\_Ridley](https://help.galaxyproject.org/u/Michael_Ridley)\ **Replies:** 4\ **Last updated:** [July 15, 2019, 9:42pm UTC](https://help.galaxyproject.org/t/downloading-large-files/1717 "2019-07-15T21:42:32Z")
Hello, Ive been trying to download a large collection ~32GB of alignments, and despite attempts, ive not been able to download more than a GB before it cuts out. this includes browser and wget options. Any advice? --- ## [Changing datatype while job is running](https://help.galaxyproject.org/t/changing-datatype-while-job-is-running/1564)
**Author:** [@michele.dellab](https://help.galaxyproject.org/u/michele.dellab)\ **Replies:** 1\ **Last updated:** [June 18, 2019, 3:18pm UTC](https://help.galaxyproject.org/t/changing-datatype-while-job-is-running/1564 "2019-06-18T15:18:06Z")
Hi all, I started a job yesterday (trimming, correction and assembly of reads with Canu), and I would like to run Nanoplot to show the statistics of the reads. The datasets I uploaded have been described as sdf datatyp… --- ## [Get unsanitized access to tags in the tool xml](https://help.galaxyproject.org/t/get-unsanitized-access-to-tags-in-the-tool-xml/1363)
**Author:** [@scholtalbers](https://help.galaxyproject.org/u/scholtalbers)\ **Replies:** 6\ **Last updated:** [May 31, 2019, 9:15am UTC](https://help.galaxyproject.org/t/get-unsanitized-access-to-tags-in-the-tool-xml/1363 "2019-05-31T09:15:55Z")
I’m currently using the following line to get tags of datasets to the underlying tool: #set tags = ','.join(str(t.value) for t in $dataset.tags) This however this does not return the original tags, they get truncated (… --- ## [edgeR error for paired differential expression analysis](https://help.galaxyproject.org/t/edger-error-for-paired-differential-expression-analysis/543)
**Author:** [@m93](https://help.galaxyproject.org/u/m93)\ **Replies:** 3\ **Last updated:** [February 9, 2019, 1:16am UTC](https://help.galaxyproject.org/t/edger-error-for-paired-differential-expression-analysis/543 "2019-02-09T01:16:30Z")
I am trying to use edgeR to perform a differential expression analysis. This is a paired analysis (samples are in pairs - their healthy vs their diseased tissues). Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/iuc/edger/… --- ## [FTP Upload stops after 70G](https://help.galaxyproject.org/t/ftp-upload-stops-after-70g/485)
**Author:** [@dcissell](https://help.galaxyproject.org/u/dcissell)\ **Replies:** 3\ **Last updated:** [January 22, 2019, 12:06am UTC](https://help.galaxyproject.org/t/ftp-upload-stops-after-70g/485 "2019-01-22T00:06:40Z")
We are trying to upload BAM(hg19) and fastq.gz files with FTP, but the upload stops after about 70G of the files have been uploaded. Our file sizes are about 95-140G in size. How can we get these files uploaded to useGa… --- ## [Uploading file to Galaxy with Bioblend not working](https://help.galaxyproject.org/t/uploading-file-to-galaxy-with-bioblend-not-working/249)
**Author:** [@m93](https://help.galaxyproject.org/u/m93)\ **Replies:** 3\ **Last updated:** [January 19, 2019, 12:37am UTC](https://help.galaxyproject.org/t/uploading-file-to-galaxy-with-bioblend-not-working/249 "2019-01-19T00:37:38Z")
UPDATE: I originally posted before Christmas but my posts now has updates: reflecting the use of the original Bioblend API vs the OO BioBlend API). with details about manual upload to Galaxy GUI I am trying to use Bio… --- ## [Is it possible to have links to data instead of having galaxy copy the data](https://help.galaxyproject.org/t/is-it-possible-to-have-links-to-data-instead-of-having-galaxy-copy-the-data/470)
**Author:** [@spooknick](https://help.galaxyproject.org/u/spooknick)\ **Replies:** 1\ **Last updated:** [January 18, 2019, 3:29pm UTC](https://help.galaxyproject.org/t/is-it-possible-to-have-links-to-data-instead-of-having-galaxy-copy-the-data/470 "2019-01-18T15:29:48Z")
I’ve installed a galaxy instance on a machine that doesn’t have a lot of storage room, as we have a very efficient NAS. My idea was to mount each user’s NAS volume on that server and have it linked somehow to the user’s … --- ## [How to stop uploading a file on GALAXY?](https://help.galaxyproject.org/t/how-to-stop-uploading-a-file-on-galaxy/294)
**Author:** [@Roopali\_Singh](https://help.galaxyproject.org/u/Roopali_Singh)\ **Replies:** 1\ **Last updated:** [December 28, 2018, 4:14pm UTC](https://help.galaxyproject.org/t/how-to-stop-uploading-a-file-on-galaxy/294 "2018-12-28T16:14:20Z")
Hi I have accidentally put wrong files for upload and the size is too big so I need to cancel the upload. How can I do that? Please help. -Roopali --- ## [Fatal error: exit code 1 () using bowtie2](https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-bowtie2/267)
**Author:** [@Roopali\_Singh](https://help.galaxyproject.org/u/Roopali_Singh)\ **Replies:** 3\ **Last updated:** [December 20, 2018, 5:43am UTC](https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-bowtie2/267 "2018-12-20T05:43:11Z")
Hi I am using bowtie2 for mapping of paired-end fastq files. However, I keep getting the error message as: fatal error: exit code 1 () \[bam\_sort\_core\] merging from 0 files and 6 in-memory blocks… I don’t understand w… [Next page](https://help.galaxyproject.org/tag/dataset/40.md?match_all_tags=true&page=1&tags%5B%5D=dataset)