Illumina Paired End Data Minimum Maximum Distance

[friedtofu]

Hello,

I am very new to sequencing and de novo assemblies. I am using CLC Genomics Workbench and am importing my fastq files.

It is asking for paired end minimum distance and maximum distance. I do not know how to calculate that.
Here is my information:

The Machine was the Illumina MiSeq.

The quality score selected, Illumina 1.8.

-----------(Read1)-----------250bp---------------------> gap <----------------------250bp---------(Read2)------------

My library size was 960, which breaks down as follows:

[ Illumina Specific Adapters, 60bp ]----------------------250bp---------------------> gap (~340bp) <----------------------250bp---------------------[ Illumina Specific Adapters, 60bp ]

Thank you for your time

[GenoMax]

Can't you use the "auto detect paired end distance" option for the first try?

[friedtofu]

Thank you for the speedy reply!

Yes, I read in the CLC manual about auto-detection of distances but I can't find where to perform this function.
When I try to import my Illumina files these are the windows I see.

[GenoMax]

What version of CLC are you using? I see that option in the latest 7.5.

[friedtofu]

CLC Genomics 7.5.1

Are they asking for the gap distance? If it is, my gap distance between reads is ~340bp, +/- 100bp so I should put min. 250 and max at 450?

I see the option for auto detection of distances when I perform de novo assembly, so maybe the numbers that I put in when I import isn't necessarily the most important?

[GenoMax]

Ah I see you are referring to the first screen.

Generally people have inserts in the 300-500 bp range. If you really have inserts that are ~800 bp then you could increase the numbers as noted above in your post.