Hi,

I am trying to parse a BAM file using readAligned. It gives me an error of incorrect number of reads. How can I resolve this error. My command is as follows. The BAM file was generated by aligning to reference fasta file using Bowtie2.

reads = readAligned("input.bam", type = "Bowtie")

Will appreciate any help!!

Probably you want instead to explore GenomicAlignments::readGAlignments() and similar; readAligned() is for 'legacy' formats that you are unlikely to encounter in a modern analysis.