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DESeq2 or EdgeR or Limma without replication
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9
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5093
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February 14, 2025
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Trinity problems? Use rnaSPAdes instead!
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14
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751
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April 13, 2024
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Fastq unavailable -- Tool does not recognize inputs? How to check why
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10
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1224
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November 10, 2023
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FreeBayes variant calling and Snpeff variant annotation
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19
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901
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September 17, 2024
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Visualize with Krona
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12
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314
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August 6, 2025
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GTN Transcriptomics Hands-on: Genome-wide alternative splicing analysis. Troubleshooting reference data choices!
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27
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315
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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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147
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September 25, 2025
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Troubleshooting resources for errors or unexpected results
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0
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11312
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November 28, 2018
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What should I do if my data exceeds the given 250GB of storage?
I’m 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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2442
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August 12, 2024
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Scheduling recurrent workflows
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8
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281
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March 26, 2024
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Avoid :warning: **Liftover** and try using a **CrossMap** tool instead
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3
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968
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September 25, 2025
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How to get faster help with your question
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2
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1078
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November 24, 2025
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Avoid :warning: **Liftover** and try using a **CrossMap** tool
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3
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753
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September 25, 2025
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3
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709
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December 5, 2024
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MAF tools in Galaxy: step by step publication with an example shared history
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8
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721
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June 15, 2023
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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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803
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January 30, 2024
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DEseq2 understanding the log2 fold change
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3
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888
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September 27, 2024
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Getting Data into Galaxy
Data Upload
Use the Upload tool to load datasets into your history
:arrow_up:
Files from your computer using Choose local files
Files with a public URL using Paste/Fetch data
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0
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1753
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September 29, 2023
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Usage help -- single end versus paired end BAM options
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5
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714
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November 10, 2023
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Private Galaxy Servers
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0
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1720
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September 28, 2023
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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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815
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May 16, 2024
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Issue with StringTie Output File when using DESeq2 option
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5
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656
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July 22, 2025
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Public Galaxy Servers
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0
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1551
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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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1503
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January 29, 2024
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Trinity and reads "smaller than 25 base pairs"
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2
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701
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December 20, 2023
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Error when running DeSeq2: help resources and input strategies
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4
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472
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July 22, 2025
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Length of Quality Sequence and Length of read do not match
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1
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712
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April 18, 2025
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User Account Quotas, Memory and Concurrent jobs at UseGalaxy.eu
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4
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142
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April 16, 2025
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Stringtie invalid escape sequence
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2
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561
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May 16, 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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581
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June 6, 2024
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Missing "paired" input for fastp tool
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8
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270
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February 24, 2025
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Account problem
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1
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310
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March 18, 2024
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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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341
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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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262
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September 27, 2024
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Error with HTseq RNAseq read count
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1
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356
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November 17, 2023
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Navigating your data storage: existing data, new data, and different storage space options with screenshots!
The program has been permanently deleted, but it still occupies 250GB of memory.How should this problem be solved?
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3
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235
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October 27, 2025
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Kraken2 Database Fungi
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4
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200
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October 13, 2025
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Assembly statistics in reference based RNA seq analysis_tools
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1
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294
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September 6, 2023
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Downloading SnpEff database into history: Create database instead!
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3
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203
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July 18, 2025
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Job delays? How to check your job queues and how to work at multiple public UseGalaxy servers
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6
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149
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August 8, 2025
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Read normalization
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4
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177
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July 22, 2025
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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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173
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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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218
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October 31, 2024
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Allowlist guidence
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7
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133
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March 4, 2025
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Qiime2 import troubleshooting: Retain original Illumnia file names + use simple list collection
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2
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115
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August 8, 2025
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Correcting errors with NCBI FCS GX Foreign Contamination Screening assembled genomes
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1
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136
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July 17, 2025
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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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192
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September 17, 2024
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BAM index, fasta indexes, display applications, custom genome builds, IGV
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3
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158
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September 22, 2025
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Quality Control Start Here! multQC issue and guidance?
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1
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221
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March 3, 2025
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How to solve problems in edgeR?
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2
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98
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March 13, 2025
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