what does “properly paired” mean？

[raving]

Hi, everyone!

I mapped a paired-end RNA-seq data with Tophat, but the properly paired reads is extremely little (about 5%), can anyone tell me what “properly paired” means and this 5% percentage means？

I filter the original .bam file accepted_hits.bam generated by Tophat with the following command:
samtools view - f 2 accepted_hits.bam -b > flt.bam

Thanks~

[Jeremy]

Properly paired means that the read orientation goes F> ---gap --- < R and that the gap is roughly the expected size, 200-400 bp.

[raving]

Properly paired means that the read orientation goes F> ---gap --- < R and that the gap is roughly the expected size, 200-400 bp.

Hi,
Thanks, and

1) when mapping, I set "-r 150" option, does it mean the gap is 150bp?
2) if the segment contains introns , then we maped the cDNA to the genome, can it properly paired?
3) the column 7 and 8 in bam file are "Mate reference sequence name" and "1-base Mate Position" , are they the mapping information of another end read? or something else?

Thanks~~