Topics tagged custom-build

Topic	Replies	Views	Activity
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
How to view a result through IGV? usegalaxy.org support custom-genome , igv , custom-build	4	26	January 7, 2026
Request for the add of genome reference-index , custom-genome , custom-build , resources	1	23	December 10, 2025
Is a "?" in featureCounts' database field a problem when using a non-built-in genome? usegalaxy.org support custom-genome , transcriptomics , igv , custom-build	1	55	November 24, 2025
BAM index, fasta indexes, display applications, custom genome builds, IGV Resources custom-genome , mapping , igv , custom-build , resources	3	150	September 22, 2025
HISAT2 and RNA STAR reference genomes usegalaxy.org support custom-genome , transcriptomics , reference-genome , custom-build	2	48	April 25, 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
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
Inquiry about lettuce genome Resources reference-index , custom-genome , reference-annotation , reference-genome , custom-build , resources	2	112	October 7, 2024
I am using HISAT2, but my reference genome Rickettsia rickettsii is missing in the dropdown list. custom-genome , mapping , custom-build	15	172	August 23, 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
Bowtie2 brucella reference usegalaxy.eu support custom-genome , custom-build , tool-help	1	42	August 13, 2024
FreeBayes variant calling and Snpeff variant annotation Resources freebayes , custom-genome , custom-build , resources , tool-help , variant-analysis , snpeff , snpeff_build_gb	19	898	September 17, 2024
How database assignments are used to access a fasta index: custom genomes, custom builds, server indexes Resources fasta-manipulation , database , reference-index , custom-genome , galaxy-local , troubleshooting , custom-build , resources	2	192	September 17, 2024
hicBuildMatrix_not_working usegalaxy.eu support custom-build	1	116	March 12, 2024
Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at Resources fasta-manipulation , custom-genome , reference-genome , custom-build , resources	5	803	January 30, 2024
Reference Genome usegalaxy.org support custom-genome , reference-genome , custom-build	7	710	January 29, 2024
bedgraph-to-bigwig error usegalaxy.eu support custom-genome , macs2 , chrominfo , custom-build	3	471	November 14, 2023
Would it be possible for galaxy to include Camelus dromedarius reference genome in built in index ? reference-index , custom-genome , reference-genome , custom-build	4	407	August 16, 2023
RNA star with reference genome from history error usegalaxy.eu support custom-genome , transcriptomics , reference-annotation , reference-genome , custom-build , deseq2 , rna_star	2	351	July 22, 2025
CHM13 T2T genome not found in options for some tools usegalaxy.org support database , custom-genome , macs2 , mapping , igv , custom-build	10	1083	July 20, 2023
Expanding the built-in reference genomes usegalaxy.eu support custom-genome , reference-annotation , reference-genome , custom-build	2	371	July 12, 2023
missing reference genome (Aedes aegypti AaegL5.0) usegalaxy.org.au support reference-index , custom-genome , mapping , transcriptomics , custom-build , featurecounts	5	402	June 13, 2023
version and source of the galaxy built-in genome usegalaxy.eu support reference-index , custom-genome , reference-genome , cvmfs , custom-build	2	1024	May 5, 2023
Source of built in reference genomes usegalaxy.eu support custom-genome , reference-genome , cvmfs , custom-build	1	478	May 5, 2023
Unresponsive page when load fasta file to build rice (Oryza sativa) genome usegalaxy.org support custom-genome , mapping , custom-build , server-status	1	295	April 13, 2023
Genome build for dog in RNA STAR usegalaxy.eu support reference-index , custom-genome , reference-genome , custom-build	5	426	March 20, 2023
Adding new Reference genomes to the DeepVariant deep learning-based variant caller usegalaxy.eu support custom-genome , mapping , transcriptomics , reference-annotation , reference-genome , custom-build , featurecounts	1	796	January 26, 2023
how to index the Tetrahymena genome? custom-genome , custom-build	4	821	January 26, 2023