Description Usage Arguments Value Author(s) Examples
unique aligned reads = total number of reads that are not secondary; uniquely aligned reads without duplicates = total number of reads that are not secondary and not duplicates; duplicate reads = total number of reads that are duplicates;
1 | SummarizeUniqueReads(BamFilePath)
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BamFilePath |
location of aligned bam file. Corresponding bai index file must be in the same directory. |
A data.frame containing a summary of the unique reads from bam file. Duplicate reads are defined as having identical pos and cigar values.
Nathaniel J. Madrid, Jason Byars
1 2 | BamFilePaths <- dir(path="/home/ubuntu/Projects/RNAseqPackage/bams", pattern=".*.bam$", full.names=T)
UniqueReadsDF = SummarizeUniqueReads(BamFilePaths[1])
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