dear developers I have performed a gapped alignment of my illumina reads. I now want to analyze the output by accessing the CHROMOSOME and POSITION information contained in the BAM file. I therefore uploaded the BAM using readAligned(), but found that all those reads aligning to the reference genome with a GAP are missing. However, when using readGappedAlignments(), I loose information crucial to my analysis (i.e., chromosome, position). Is there any way to upload into R GAPPED alignments while preserving read ID, chromosome, position etc? thanks, Daniel Berner
[Bioc-devel] accessing gapped alignment
2 messages · Daniel.Berner at unibas.ch, Martin Morgan
On 12/20/2010 05:27 AM, Daniel.Berner at unibas.ch wrote:
dear developers I have performed a gapped alignment of my illumina reads. I now want to analyze the output by accessing the CHROMOSOME and POSITION information contained in the BAM file. I therefore uploaded the BAM using readAligned(), but found that all those reads aligning to the reference genome with a GAP are missing. However, when using readGappedAlignments(), I loose information crucial to my analysis (i.e., chromosome, position). Is there any way to upload into R GAPPED alignments while preserving read ID, chromosome, position etc?
Rsamtools::scanBam lets you read whatever you want, returning a list with the corresponding data. library(Rsamtools) example(scanBam) What is that you want to do with the data once in R? Martin
thanks, Daniel Berner
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