script/debug-RNABamStats.R
In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data
## posSpecErrorBam function
param = ScanBamParam(what=c("qname", "seq"),
flag=scanBamFlag(isUnmappedQuery=FALSE, isSecondaryAlignment=FALSE, isDuplicate=FALSE))
bamGA <- readGAlignments("/srv/gstore/projects/p2179/STAR_13239_2018-03-27--13-42-28/ILC3_D2_S16.bam", param=param)
genome <- readDNAStringSet("/srv/GT/reference/Homo_sapiens/Ensembl/GRCh38.p10/Sequence/WholeGenomeFasta/genome.fa")
errShort <- posSpecErrorBam(bamGA, genome)
uzh/ezRun documentation built on May 9, 2024, 6:16 p.m.
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## posSpecErrorBam function
param = ScanBamParam(what=c("qname", "seq"),
flag=scanBamFlag(isUnmappedQuery=FALSE, isSecondaryAlignment=FALSE, isDuplicate=FALSE))
bamGA <- readGAlignments("/srv/gstore/projects/p2179/STAR_13239_2018-03-27--13-42-28/ILC3_D2_S16.bam", param=param)
genome <- readDNAStringSet("/srv/GT/reference/Homo_sapiens/Ensembl/GRCh38.p10/Sequence/WholeGenomeFasta/genome.fa")
errShort <- posSpecErrorBam(bamGA, genome)
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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