#15 How to generate Illumina amplicon reads with pairwise overlap?

[Anonymous]

We want to generate the paired-end amplicon reads. Reads of a pair have a certain overlap. We found that the option -insert_dist must be longer than read length. That is, it looks like that it is impossible to generate such kind of paired-end reads. Could we have your instructions how to simulate the Illumina amplicon data?

[floflooo]

Use the -id <insert_dist> option.</insert_dist>

From the manpage: "The insert is defined in the biological sense, i.e. its length includes the length of both reads and of the stretch of DNA between them". Thus by definition, a Grinder read cannot be longer than the insert length. The Grinder definition contrasts with the other definition, in which the insert is defined to be the section of DNA between the reads only.

In Grinder, you should give a small enough insert size (relative to the read length) to obtain overlapping paired reads. If your insert length is 250 bp and your reads are 100 bp long, then the reads are separated by 50 bp. If you use an insert length of 150 bp and your reads are 100 bp long, you have an overlap of 50 bp.

Give it a try and let me know how you go. Cheers,

Florent