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DESeq2 or EdgeR or Limma without replication
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9
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4948
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February 14, 2025
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Fastq unavailable -- Tool does not recognize inputs? How to check why
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10
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1122
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November 10, 2023
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Trinity problems? Use rnaSPAdes instead!
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14
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472
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April 13, 2024
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FreeBayes variant calling and Snpeff variant annotation
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19
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584
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September 17, 2024
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Visualize with Krona
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12
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186
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August 6, 2025
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Issue with rnaQUAST tool
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27
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88
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August 19, 2025
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ATAC Seq wig to bigwig transformation of MACS2 data
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9
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70
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September 25, 2025
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Troubleshooting resources for errors or unexpected results
How to troubleshoot your work in Galaxy, and how to ask for help!
:mag_right: Review your Job Details ā inputs + parameters + logs using the i-icon inside of any dataset.
:mortar_board: Learn with a tutorial and custom…
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0
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11071
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November 28, 2018
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What should I do if my data exceeds the given 250GB of storage?
Iām working on a transciptomics data which will probably exceed the given 250GB data. Is there any possible solution to this? for example increasing my storage?
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1
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1822
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August 12, 2024
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Scheduling recurrent workflows
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8
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212
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March 26, 2024
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How to get faster help with your question
How to get faster help with your question
We love details! :scientist: Consider Sharing your History or posting screenshots of your Job Information Details page. Questions with details attract the fastest replies!
Pleas…
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0
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861
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January 12, 2024
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Avoid :warning: **Liftover** and try using a **CrossMap** tool instead
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3
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927
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September 25, 2025
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Avoid :warning: **Liftover** and try using a **CrossMap** tool
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3
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704
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September 25, 2025
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Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at
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5
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729
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January 30, 2024
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How to see the UseGalaxy.eu job queue statistics
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3
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480
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December 5, 2024
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Usage help -- single end versus paired end BAM options
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5
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631
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November 10, 2023
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Private Galaxy Servers
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0
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1516
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September 28, 2023
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Getting Data into Galaxy
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0
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1451
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September 29, 2023
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Issue with StringTie Output File when using DESeq2 option
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5
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583
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July 22, 2025
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Public Galaxy Servers
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0
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1344
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September 28, 2023
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Reference genomes at public Galaxy servers: GRCh38/hg38 example
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0
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1247
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January 29, 2024
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How to find the reference transcriptome for analysis tools: GRCh38/hg38 example
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3
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607
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May 16, 2024
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Trinity and reads "smaller than 25 base pairs"
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2
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673
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December 20, 2023
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DEseq2 understanding the log2 fold change
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3
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498
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September 27, 2024
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Length of Quality Sequence and Length of read do not match
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1
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692
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April 18, 2025
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Stringtie invalid escape sequence
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2
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502
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May 16, 2024
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Error when running DeSeq2: help resources and input strategies
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4
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359
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July 22, 2025
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Account problem
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1
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277
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March 18, 2024
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SPAdes error -- running out of memory/not enough memory allocated for job
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1
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467
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June 6, 2024
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User Account Quotas, Memory and Concurrent jobs at UseGalaxy.eu
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4
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78
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April 16, 2025
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Error with HTseq RNAseq read count
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1
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325
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November 17, 2023
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This job was terminated because it used more memory than it was allocated
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2
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230
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July 22, 2024
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Faster Download and Extract Reads in FASTQ and ENA reads are slightly different
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3
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198
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September 27, 2024
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Missing "paired" input for fastp tool
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8
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127
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February 24, 2025
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Assembly statistics in reference based RNA seq analysis_tools
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1
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263
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September 6, 2023
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How database assignments are used to access a fasta index: custom genomes, custom builds, server indexes
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2
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155
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September 17, 2024
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Job execution timing and computational resources: any tool, any public Galaxy server
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4
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112
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July 18, 2024
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How to analyze trimmed reads by Shovill Faster Spades Assembly tool
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2
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137
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October 31, 2024
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Downloading SnpEff database into history: Create database instead!
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3
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88
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July 18, 2025
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Need help with the dataset error report on MITOS (version 1.1.7) de-novo annotation tool of metazoan mitochondrial genomes
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5
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71
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September 24, 2024
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Correcting errors with NCBI FCS GX Foreign Contamination Screening assembled genomes
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1
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62
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July 17, 2025
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An error of limma
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1
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106
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May 2, 2024
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How to solve problems in edgeR?
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2
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47
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March 13, 2025
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Need help to run Phyloseq in Galaxy to characterize microbial taxa
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2
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77
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September 17, 2024
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Uploading large file problem
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4
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56
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July 2, 2025
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Ensembl gene annotation gtf for rat problem with RNA STAR
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2
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72
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February 26, 2025
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Inquiry about lettuce genome
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2
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71
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October 7, 2024
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Read normalization
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4
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55
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July 22, 2025
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Resolving memory failures with SPAdes
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2
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68
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March 17, 2025
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FAQ: NCBI reference data
:speech_balloon: How to find NCBI Reference data?
Q: Where can I find the URL links to a reference genome FASTA, annotation, or GenBank file?
A: Use the NCBI Genome Assembly page for the organism of interest ā for examp…
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0
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118
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June 12, 2025
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