Build canine dna.primary_assembly.fa for kb ref
I am following the instruction to build the index using kb.
The command should be
kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa -c1 cdna_t2c.txt -c2 /
intron_t2c.txt --workflow lamanno -n 8 /
Mus_musculus.GRCm38.dna.primary_assembly.fa.gz /
Mus_musculus.GRCm38.98.gtf.gz
In Ensembl dog genome, there is no such file as dna.primary_assembly.fa.gz. They're separate files (by chromosome) as shown here.
How could I create a dna.primary_assembly.fa.gz for canine genome that includes all chromosomes?
Thanks!
1 answer
I've found the answer. It turns out the Readme in Ensemble says "If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent."
Therefore, I can use the 'Canis_lupus_familiaris.ROS_Cfam_1.0.dna.topleve.fasta.gz' here
Log in to answer this question.
More posts like this
-
RNA velocity similar mtx for spliced and unspliced region (dropseq)
written by akilabioinfo •
-
Kallisto bustools index
written by Shawn •
-
kallisto preprocessing-Error: unspliced. bus has no BUS records
written by gabriella.wangyi1986 •
-
Problem in single cell RNA velocity analysis using kb_python
written by Mohamed Omar •
You should be able to
catthe files together.