Q: I have run DeletionID but many genes are being returned in the output report. Are all of these genes in the list depleted from my sample?
First check your sequencing coverage. When it is low, DeletionID can misidentify or identify many more knockout regions than are actually present.
Is your assay chromatin based? DeletionID does not work well with RNAseq datasets due to the heavily skewed distribution of reads across the genome. Please read the disclaimer above for more information.
Q: I have data from a human/mouse deletion that I wish to identify. Do you have a reference database for genes from the mm10 or hg19 genome assemblies?
DeletionID has not been benchmarked against samples from human or other organisms with large genomes. Please see the caution note above for more information.