bwa mapping question

[aleuUH]

Hi

I was wondering if anyone has encountered this before: When i mapped a fastq file to a reference, bwa will give me both reads that are mapped as well as reads that are unmapped. However when i checked the fastq file, there are reads that were not included in the bam file as either mapped or unmapped.

Is this normal?

Thanks

[lidd77]

Perhaps such these reads you said are unpaired ?