View source: R/app-RnaBamStats.R
getDupRateFromBam | R Documentation |
Read in a BAM file and count the tags falling on the features described in the GTF file
getDupRateFromBam(bamFile, param = NULL, gtfFn,
stranded = c("both", "sense", "antisense"),
paired = FALSE, threads = 1)
bamFile |
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param |
ezRun param list. |
gtfFn |
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stranded |
|
paired |
|
threads |
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It uses the implementation of package dupRadar.
A data.frame
of counts on features, with and without taking into account multimappers/duplicated reads
Ge Tan
Sayols S, Scherzinger D and Klein H (2016). "dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data." BMC Bioinformatics, 17, pp. 428. doi: 10.1186/s12859-016-1276-2, http://dx.doi.org/10.1186/s12859-016-1276-2.
## Not run:
bamFile <- "/srv/gstore/projects/p2438/STAR_18564_2017-06-12--13-46-30/26EV_BL_A.bam"
gtfFn <- "/srv/GT/reference/Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-05-31/Genes/genes.gtf"
stranded <- "antisense"
paired <- FALSE
threads <- 4
resBam <- getDupRateFromBam(bamFile=bamFile, gtfFn=gtfFn,
stranded=stranded,
paired=paired, threads=threads)
## End(Not run)
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