Topics tagged reference-annotation

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	341	June 12, 2025
Does using the same gtf file for RNA Star and featureCounts cause problems? usegalaxy.org support workflow , troubleshooting , reference-annotation , genome-annotation , featurecounts	1	16	June 24, 2026
Extracting data from a .gff3 file text-manipulation , reference-annotation , resources	3	33	May 18, 2026
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	42	February 19, 2026
Rat Featurecount Selection troubleshooting , reference-annotation , featurecounts	2	33	January 28, 2026
Using CHM13v2.0 T2T and mm39 gene annotations for RNASeq Analysis usegalaxy.eu support transcriptomics , reference-annotation , reference-genome , tool-help , deseq2 , featurecounts	3	189	December 3, 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	943	May 16, 2024
Help with RNA Star, Featurecounts, and reference annotation choices Resources transcriptomics , reference-annotation , resources , featurecounts , iwc-workflows	1	209	August 19, 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	51	August 5, 2025
Adding a New Reference Genome for Cannabis sativa usegalaxy.org support custom-genome , reference-annotation , reference-genome	1	56	July 29, 2025
Want to add a new organism for HISAT2 analysis usegalaxy.org support reference-index , reference-annotation , reference-genome	1	38	June 12, 2025
BRAKER3 fails with 'Genemark not installed' error usegalaxy.eu support reference-annotation , tool-help , genmark , braker3 , genemark	1	173	May 5, 2025
RUVSeq:Fatal error: An undefined error occurred, please check your input carefully and contact your administrator Resources transcriptomics , reference-annotation , resources , tool-help , ruvseq	1	38	April 18, 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	10	192	March 14, 2025
Ensembl gene annotation gtf for rat problem with RNA STAR Resources troubleshooting , mapping , reference-annotation , reference-genome , resources	2	160	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	42	February 19, 2025
Custom reference genome annotation usegalaxy.org support custom-genome , reference-annotation , reference-genome	5	1267	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	66	February 10, 2025
FEELnc troubleshooting troubleshooting , reference-annotation , lncrna	5	221	February 10, 2025
I can not get counts transcriptomics , reference-annotation , reference-genome , tool-help , rna_star	5	102	January 31, 2025
Feature count on exon level instead gene level usegalaxy.eu support transcriptomics , reference-annotation , rna-seq , featurecounts	3	224	January 28, 2025
How to get galaxy to call transcript types from gene symbols? usegalaxy.org.au support text-manipulation , transcriptomics , reference-annotation	1	48	January 15, 2025
Built-in reference genome of domestic water buffalo usegalaxy.org.au support reference-index , reference-annotation , reference-genome	1	78	January 6, 2025
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	57	November 25, 2024
Reference annotation for TAIR10 reference-index , reference-annotation , reference-genome , reference-transcriptome	1	214	November 6, 2024
Gene ID's being filtered out in ChipSeq analysis usegalaxy.org.au support chip-seq , data-manipulation , reference-annotation , tool-help , get_flanks1	5	94	November 4, 2024
Feature counts built-in annotation file - no options available transcriptomics , reference-annotation , tool-help , featurecounts	2	250	October 28, 2024
Inquiry about lettuce genome Resources reference-index , custom-genome , reference-annotation , reference-genome , custom-build , resources	2	130	October 7, 2024
How can i use SILVA_138.2 latets as a reference to align.seqs tool in GALAXY Server? usegalaxy.eu support gtn-tutorial , metagenomics , reference-annotation , tool-help	1	62	October 4, 2024
Genes from my reference genome are not annotated in output files. Trying to get read count per gene/abundant gene list usegalaxy.org support troubleshooting , reference-annotation , rna-seq	1	39	October 1, 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…