[BioC] missing reads in alignerBAM

Martin Morgan mtmorgan at fhcrc.org
Fri Dec 17 13:58:14 CET 2010

On 12/17/2010 12:55 AM, Daniel.Berner at unibas.ch wrote:
> hi list
> When I align the N reads contained in my Illumina fastq using NovoAlign,
> convert the resulting SAM output to BAM using Samtools, and then upload
> the BAM file using readAligned (ShortRead), the resulting AlignedRead
> object contains fewer than N reads. Reconverting the BAM to SAM and
> counting the lines using wc -l, however, indicates there are still N
> reads in the BAM. Hence it appears that during upload into R, some reads
> are lost. The AlignedRead object, however, will contain exactly N reads
> when I perform the alignment using bowtie instead of NovoAlign.
> Any idea/comment on why reads are missing?

Hi Daniel --

readAligned and the AlignedRead class represents reads aligned without
gaps (see ?readAligned, type="BAM"). You can use
GenomicRanges::readGappedAlignments (alignment coordinates without
sequence information) or Rsamtools::scanBam to input all data.


> Thanks, Daniel
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

More information about the Bioconductor mailing list