next segment.

[ardmore]

Here are some terms definition from samtools manual.

Template: A DNA/RNA sequence part of which is sequenced on a sequencing machine or assembled
from raw sequences.
Segment: A contiguous (sub)sequence on a template which is sequenced or assembled. For sequencing
data, segments are indexed by the order in which they are sequenced. For segments of an
assembled sequence, they are indexed by the order of the leftmost coordinate on the assembled
sequence.

Then

RNEXT: Reference sequence name of the NEXT segment in the template. For the last segment,
the next segment is the rst segment in the template.

My question is what is next segment? My major is not bioinformatics, so sorry for the silly question.

Thanks a lot.

[swbarnes2]

All of this is new in the last few years, so its not like any of us learned this in classes.

In general, most of the next-gen technologies produce two reads per DNA fragment, one at either end of it. But some technologies, (I think Ion Torrent can be set up to work like this), can produce multiple read sequences for each DNA fragments, separated by blank spaces, where the DNA sequence isn't determined.

So unless you are using a technology like that, your next segment is just your read 2 of that DNA fragment.