Distance Between Mate Pairs

Question

[Mohamed]

Hi,

I am new to the bio-informatics area and need some help.

GATK uses BWA to generate single ended alignments. I have the following question with respect to the mate pair information available in the alignment output (BAM file).

The SAM specification refers this as template. The alignment output has fields for the position of the next segment in the template (PNEXT) and template length (TLEN).

1. How many reads (segments) can a template have ?

2. Is there any maximum distance between the first and the last segment in the template ? I meant can I safely say that template length can never be greater than some 'x'.

3. I initially thought that mate pair information will be available only for pair-end alignment. But now I realized that mate pairs are different from paired-end reads. Please correct my understanding.

Thanks in advance..

Answer 1

[Istvan Albert]

The mate pairing refers to the sequencing technology that makes it possible to keep track of both ends of a sequenced DNA fragment. The distance between mate pairs is a sequencing platform specific information that depends on the methodology that is employed.

The words mate-pair and paired-end are often used interchangeably and there is not specific nomenclature that would distinguish between the two. Moreover technology changes as well. Make sure to read up on your documentation to understand the orientation of the pairs that you are getting.