Topics tagged reference-genome

Topic	Replies	Views	Activity
FAQ: NCBI reference data Resources reference-index , reference-annotation , reference-genome , resources :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…	0	247	June 12, 2025
Genome update sus scro: how to use a custom genome! usegalaxy.org support reference-index , custom-genome , troubleshooting , reference-annotation , reference-genome , custom-build	2	15	February 19, 2026
Why MACS2 callpeak for Cut&Run analysis shows error? macs2 , reference-genome	3	53	December 8, 2025
Using CHM13v2.0 T2T and mm39 gene annotations for RNASeq Analysis usegalaxy.eu support transcriptomics , reference-annotation , reference-genome , tool-help , deseq2 , featurecounts	3	100	December 3, 2025
Base mismatch in arabidopsis tair 10 ref genome usegalaxy.eu support reference-genome	3	42	November 12, 2025
Reference genome using BWA-MEM usegalaxy.org support bwa-mem , reference-genome	4	70	November 11, 2025
How to find the reference transcriptome for analysis tools: GRCh38/hg38 example Resources troubleshooting , reference-annotation , reference-genome , resources , tool-help , reference-transcriptome , salmon , kallisto_quant	3	809	May 16, 2024
GTN Transcriptomics Hands-on: Genome-wide alternative splicing analysis. Troubleshooting reference data choices! Resources transcriptomics , reference-genome , resources , tool-help , reference-transcriptome , rna_quast	27	311	August 19, 2025
Error occurred in dataset while running the workflow usegalaxy.eu support reference-genome	4	47	August 11, 2025
Newly launched BN rat genome assembly GRCr8 into the reference genome list? usegalaxy.eu support reference-index , custom-genome , reference-annotation , reference-genome	1	46	August 5, 2025
Adding a New Reference Genome for Cannabis sativa usegalaxy.org support custom-genome , reference-annotation , reference-genome	1	45	July 29, 2025
How to download the inbuilt reference genome reference-genome	1	23	July 2, 2025
Want to add a new organism for HISAT2 analysis usegalaxy.org support reference-index , reference-annotation , reference-genome	1	35	June 12, 2025
HISAT2 and RNA STAR reference genomes usegalaxy.org support custom-genome , transcriptomics , reference-genome , custom-build	2	48	April 25, 2025
Getting NCBI Reference genome indexed for tools: custom genome, reference genome, reference annotation reference-index , custom-genome , reference-annotation , reference-genome , featurecounts , reference-transcriptome	11	152	July 22, 2025
Ensembl gene annotation gtf for rat problem with RNA STAR Resources troubleshooting , mapping , reference-annotation , reference-genome , resources	2	134	February 26, 2025
Request to upload/add new version of reference genome of Aedes albopictus (Genome assembly AalbF5) usegalaxy.org support reference-index , custom-genome , reference-annotation , reference-genome , reference-transcriptome	1	41	February 19, 2025
Custom reference genome annotation usegalaxy.org support custom-genome , reference-annotation , reference-genome	6	1234	February 14, 2025
How to select a different reference genome from that already present using the tool RNA-STAR usegalaxy.org support custom-genome , reference-annotation , reference-genome , custom-build , rna_star	2	50	February 10, 2025
I can not get counts transcriptomics , reference-annotation , reference-genome , rna_star	5	88	January 31, 2025
Built-in reference genome of domestic water buffalo usegalaxy.org.au support reference-index , reference-annotation , reference-genome	1	70	January 6, 2025
RNAstar Select Reference Genome - Species Not Available - contact the Galaxy team (--genomeDir) usegalaxy.eu support custom-genome , mapping , reference-annotation , reference-genome , custom-build , reference-transcriptome	1	46	December 4, 2024
Bowtie2 reference genome of Goat (Capra Hircus) usegalaxy.org support reference-index , custom-genome , mapping , reference-annotation , reference-genome , custom-build , tool-help , reference-transcriptome , bowtie2	1	47	November 25, 2024
Files for miRNA differential expression analysis mirna , reference-genome	9	2247	November 12, 2024
Reference annotation for TAIR10 reference-index , reference-annotation , reference-genome , reference-transcriptome	1	174	November 6, 2024
Adding C. elegans WS235 ce11 reference genome to be used in RNA STAR usegalaxy.org support reference-genome	1	71	November 6, 2024
Inquiry about lettuce genome Resources reference-index , custom-genome , reference-annotation , reference-genome , custom-build , resources	2	112	October 7, 2024
Train Augustus doesn't work usegalaxy.org.au support troubleshooting , reference-annotation , reference-genome	7	247	September 10, 2024
SICER is not available for the genome. reference-index , custom-genome , reference-genome , custom-build , tool-help , peakcalling_sicer	1	70	August 13, 2024
mm10/GRCM38 genome usegalaxy.eu support reference-index , reference-genome	1	57	August 8, 2024

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…