Closed Alf-Kenz closed 1 year ago
Hi,
That is indeed the reference fasta file I have been using with scsnv for my projects.
The scsnv index
command indexes the transcriptome rather than the genome (it uses this for spliced read counts), while the full genome is used for unspliced / intergenic read counts. You can use a pre-created BWA index for the bwa index
portion as long as it's to the same genome fasta file.
The alt warnings are from BWA when running scsnv index
. I am not sure why you would be receiving them if there aren't any alts present.
The nice part is once these indices are generated you never have to use them again.
Gavin
Hi
Wowow such a fast response, thanks so much. To triple check (feel free to not respond since you answered above, I'm just planning on putting a lot of compute time into this, so wanted to be certain), I was talking about the Alt contigs logging here. As I was reading through the code, it seems like the alt contig handling comes up a moderate amount, so wanted to make sure the reference I was using had all the parts scsnv could use for the highest accuracy
HI @Alf-Kenz,
I don't specifically do anything with the ALT contigs during the alignment. But I don't think it should give any issues. If you have some problems let me know and I will try to fix them. I am working on making scSNV faster; particularly the read collapsing part. I just haven't had enough free time to work on it.
Let me know if you have any other issues and I am happy to help
Gavin
Amazing all around, thanks very much for such a fast and helpful response!
I might start running it on many hundreds of of samples, so any speedups would be great :-)
Hi,
Really nice work, I'm excited to try it on some of my data!
For normal human data, can you give advice on the exact reference you suggest/use in the paper? Would you just pull the most recent primary assembly e.g. https://ftp.ensembl.org/pub/release-109/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz? As I load it in, this logs a lot about
alt
strands (which this shows 0), should I use a different reference insteadAnd to confirm, I should run both
scsnv index
as well asbwa index
. When I was doing it for the primary assembly, it was taking a very long time, and I saw that illumina also hosts pre-indexed versions here