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DepthOfCoverage calculateCoverageOverGenes missing genes
I've been learning how to use the DepthOfCoverage to calculate coverage across genes. I noticed that some genes were covered by the bam, in the interval_list file, and in the geneList file, but were not reported in the gene_summary table. Most of these were non-coding RNAs, and in reviewing the geneList file, I noticed that for the non-coding RNAs, the Coding region start position is 1 base higher than the Coding region end position (which also put the Coding region start position higher than the Transcription end position). I adjusted the file and made the Coding region identical to the Transcription regions for the non-coding RNAs, and this resolved the issue for most of the genes. It appears that remaining genes that are still not reported in the gene_summary table, all overlap with exons or UTRs from other genes. My questions are:
- Is it the case that if two exons overlap, only one will be reported on, or is something else going on?
- What regions of the gene is the tool reporting on, the whole transcribed region, or just the coding region?
- Am I safe in changing the coding regions of non-coding RNAs to equal the transcribed region for the coverage analysis?