Expected Pair-end length parameter - GSNAP

[fongchun]

Hi,

I apologize if this question has been asked, but I can't find any clarification on this question. I've gotten no replies on the gsnap mailing list about this unfortunately.

I am looking at the --pairexpect parameter in gsnap:

-pairexpect=INT Expected paired-end length, used for calling splices in medial part of paired-end reads (default 200)

Is this referring to the inner-mate distance between the two paired-end reads? Or is it the expected insert size of the fragment that the paired-end reads are sequenced from (i.e. read length * 2 + inner-mate distance)? Or am I totally misinterpreting the meaning of this parameter?

Any help would be appreciated.

Thanks

[jebowers]

I do not know this software but in general, for many software programs, paired end length is the whole size of the insert. Generally read*2+inter-mate distance.

[fongchun]

I do not know this software but in general, for many software programs, paired end length is the whole size of the insert. Generally read*2+inter-mate distance.

Thanks for the reply. You are right. I got a direct reply from the author and it is indeed the insert size.