Hi,
I am looking for a function or accessor in the R/Bioconductor package ShortRead, or something that uses the same standard format, that is able to get me the CIGAR strings.
I'm commonly using readAligned(filename,path,type="BAM") to access BAM files in R, however I could not find on how to access the optional data using ShortRead.
I'm especially interested in "XM:Z:" (methylation call strings from recent Bismark SAM output) as a part of a standard AlignedRead object.
Many thanks in advance
I am looking for a function or accessor in the R/Bioconductor package ShortRead, or something that uses the same standard format, that is able to get me the CIGAR strings.
I'm commonly using readAligned(filename,path,type="BAM") to access BAM files in R, however I could not find on how to access the optional data using ShortRead.
I'm especially interested in "XM:Z:" (methylation call strings from recent Bismark SAM output) as a part of a standard AlignedRead object.
Many thanks in advance
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