Hello, I'm following up on a question that was asked years ago Ensembl assembly choice for RNA-Seq reference mapping
The Bos taurus references on Ensembl are separated by chromosome for the "DNA.primary.assembly", but there is no combined primary assembly for all of the chromosomes. How should one create the combined primary assembly to perform indexing using HISAT2?
Thank you!
1 answer
You can either use the "top level" file of if that is not present then you can cat the individual chromosomes to create a single "genome" file.
If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent.
See the line from the README file that I added above that you will find here: https://ftp.ensembl.org/pub/release-111/fasta/bos_taurus/dna/README
Log in to answer this question.
-
Building Salmon and STAR index using rat GRCr8 reference genome
written by Ajina •
-
HISAT2 human index and GTF file version incompatibility
written by Rituriya •
-
Forum: Sequence (annotation) databases in 2021
written by Dunois •
-
Error in getBM: accessing Ensembl annotation with biomaRt
written by celia.escher •
-
Ensembl assembly choice for RNA-Seq reference mapping
written by eoin •
-
Variant calling and linkage disequilibrium when using de novo assembles
written by avismirabilis •
-
Matching Gencode annotations to Assemblies
written by roberto.spreafico •
-
Autosomal SNPs tagging sex chromosomes?
written by Purpleone
-
How Should I Split My Bams By Chromosomes ? For Which Operations ?
written by Pierre Lindenbaum
-
Number Of Snps In Dbsnp Don'T Add Up
written by Andrea_Bio •
