How to filter paired reads that are not mapped?

[rnaeye]

Hi!,
This should be very easy but it's confusing to me. I would appreciate some help. I have paired end Illumina sequencing. I want to keep only *unmapped* reads. Additionally, if one of the mates mapped I do NOT want to keep that pair either. I want to use unmapped reads for assembly. I am running following samtools flag, am I doing the right thing?

samtools view -f4 -F8 -S input.sam > output.sam

If this is the right command, why my output.sam file has reads with chromosome names on it. Thank you very much.

[dpryan]

Unmapped reads are allowed to have chromosomes and even positions associated with them. You samtools view command is correct for extracting pairs where neither mate maps (assuming the BAM file only contains paired-end reads...which is quite likely).

[bastianwur]

There's also directly an option in bowtie2 to filter out unmapped reads into separate fastq files.