I am trying to use cnvnator on lycopersicum and it always generates 0 reads.

Question

[nikie.vos]

Hello.

I am trying to use cnvnator on lycopersicum and it always generates 0 reads. I know it should be able to run on

lycopersicum because the paper mentions cnvnator can run on non-human genomes.

I have tried several lines besides these:

/path/to/CNVnator_v0.3/src/cnvnator -root 105.dedup.realign.root \
                                    -chrom chr01 chr02 chr03 \
                                    -tree /path/to/lycopersicum/105.dedup.realign.bam
/path/to/CNVnator_v0.3/src/cnvnator -root 105.dedup.realign.root \
                                    -chrom 1 2 3 \
                                    -tree /path/to/lycopersicum/105.dedup.realign.bam
/path/to/CNVnator_v0.3/src/cnvnator -root 105.dedup.realign.root \
                                    -genome SL2.40 \
                                    -chrom chr01 chr02 chr03 \
                                    -tree /path/to/lycopersicum/105.dedup.realign.bam

Do you have any idea what I am doing wrong?

Kind regards,

Nikie vos

[Istvan Albert]

please don't delete your question once it has been answered - it may be useful for others in the future. imagine if everyone deleted their questions once answered - the site would not exist

[Ram]

I've cleaned up your post and replaced the real path to CNVnator with /path/to/cnvnator/

Answer 1

[Coryza]

Does it produce any error messages? And those 3 commands you've mentioned show inconsistency in chromosome names.

Edit: You should have used SL2.40ch00 as chromosome names etc. That should fix your problem.