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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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de novo assembled genomes #241

Open weihongqi opened 3 years ago

weihongqi commented 3 years ago

Hi,

Is it possible to use cnvnator for analyzing datasets where the reference genome is not in the list of valid genomes (NCBI36, hg18, GRCh37, hg19, mm9, hg38, GRCh38)?

When I tried it with bam files aligned against de nnvo assembled genomes (chromosome names were different from chr1, chr2 ...), the root file was generated ok.

-hist step ran for a few days, output two lines without errors: Allocating memory. Done.

the -stat step output the following error: Can't find any signal histograms.

Do I need to rename all chromosomes to chr1, chr2, ... in order to get it work? Thanks.

Kind regards,

Weihong

abyzov commented 3 years ago

Hi, yes CNVnator can be run with any genome. I know that some people successfully applied it with genomes that consisted of a number contigs. Regarding the “no signal” message. I’m not sure what is the issue. Naming shouldn’t be a problem. You can try to apply -his step to a particular contig and check for results.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

jcchacond commented 2 years ago

Dear Alexej,

When using non-chromosome level reference genomes, Is there a minimum scaffold/contig size and number to be used?

Thank you in advance, Camilo

abyzov commented 2 years ago

Hi, there is no minimum requirement for the number of scaffolds. But I would remove ignore short contigs (up to 10 lengths of the fragment size or bin size) because of the possible artifacts of read mapping at boundaries.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978