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? Thanks, Daniel

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. Martin > 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