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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 — for examp…
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0
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181
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June 12, 2025
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Using CHM13v2.0 T2T and mm39 gene annotations for RNASeq Analysis
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3
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49
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December 3, 2025
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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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725
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May 16, 2024
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Help with RNA Star, Featurecounts, and reference annotation choices
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1
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83
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August 19, 2025
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Newly launched BN rat genome assembly GRCr8 into the reference genome list?
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1
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32
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August 5, 2025
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Adding a New Reference Genome for Cannabis sativa
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1
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39
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July 29, 2025
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Want to add a new organism for HISAT2 analysis
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1
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24
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June 12, 2025
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BRAKER3 fails with 'Genemark not installed' error
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3
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116
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May 19, 2025
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RUVSeq:Fatal error: An undefined error occurred, please check your input carefully and contact your administrator
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1
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26
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April 18, 2025
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Getting NCBI Reference genome indexed for tools: custom genome, reference genome, reference annotation
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11
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104
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July 22, 2025
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Ensembl gene annotation gtf for rat problem with RNA STAR
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2
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106
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February 26, 2025
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Request to upload/add new version of reference genome of Aedes albopictus (Genome assembly AalbF5)
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1
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31
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February 19, 2025
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Custom reference genome annotation
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6
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1177
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February 14, 2025
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How to select a different reference genome from that already present using the tool RNA-STAR
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2
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30
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February 10, 2025
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FEELnc troubleshooting
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5
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206
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February 10, 2025
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I can not get counts
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5
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45
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January 31, 2025
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Feature count on exon level instead gene level
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4
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156
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July 22, 2025
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How to get galaxy to call transcript types from gene symbols?
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1
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22
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January 15, 2025
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Built-in reference genome of domestic water buffalo
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1
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44
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January 6, 2025
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RNAstar Select Reference Genome - Species Not Available - contact the Galaxy team (--genomeDir)
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1
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34
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December 4, 2024
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Bowtie2 reference genome of Goat (Capra Hircus)
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1
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39
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November 25, 2024
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Reference annotation for TAIR10
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1
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142
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November 6, 2024
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Gene ID's being filtered out in ChipSeq analysis
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5
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48
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November 4, 2024
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Feature counts built-in annotation file - no options available
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2
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216
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October 28, 2024
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Inquiry about lettuce genome
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2
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101
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October 7, 2024
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How can i use SILVA_138.2 latets as a reference to align.seqs tool in GALAXY Server?
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2
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48
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October 4, 2024
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Genes from my reference genome are not annotated in output files. Trying to get read count per gene/abundant gene list
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1
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28
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October 1, 2024
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Train Augustus doesn't work
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7
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221
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September 10, 2024
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What is the meaning of Reference Gene Model in FPKM Tools in Galaxy?
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1
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125
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August 6, 2024
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Human genome GCF_000001405 and variations
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1
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159
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July 24, 2024
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