Uploading MiSeq mate-pair in CLC Genomics Workbench

[sentausa]

Dear all,

I'm trying to import MiSeq FastQ files to CLC Genomics Workbench (version 4 point something), and I want to make sure that I'm doing the right thing. They're mate-pair data, so I choose mate-pair in the paired read information option. However, I'm not sure about the "Minimum" and "Maximum distance". How can I know the right values to enter?

The sequencing technician told me that the read length is 250 bp and the insert size is 2.9 kb. Do these values have anything to do with the minimum and maximum distance of the mate-pair information?

Your help is really appreciated.

[GenoMax]

Current version of CLC Genomics Workbench is 7.0. Is there a reason why you are using (i.e. do not have a maintenance contract) an old version such as 4.x?

Have a look at the CLC DeNovo assembly guide here: http://www.clcbio.com/files/tutorial...aired_data.pdf It explains the mate-pair data import on page 3.

[sentausa]

Thanks for your reply.

About why I'm using a 4.x version, it's just because that's what's available in our lab. About why that happens, I believe I should ask someone who is responsible there.

Thank you for pointing me to the tutorial. Unfortunately, I can't see any explanation on why we put certain values as minimum and maximum distances. Further elaboration would be really helpful.

[GenoMax]

Inserts in a typical library are never exactly the same size. You should check with the person who made the mate-pair libraries to see what would be an appropriate range to use.

CLC needs to know what distance it should allow for between the two read pairs as it tries to do assembly. So for example your 2.9 kb insert library may have inserts between 2.7 and 3.2 kb.

[sentausa]

You mean the minimum distance should be 2700 and the maximum 3200? How did you get these numbers? Thanks again.

[GenoMax]

You mean the minimum distance should be 2700 and the maximum 3200? How did you get these numbers? Thanks again.

As I said before you should ask the person who made the libraries (or QC'ed them) to see what the numbers should be. I used those numbers as examples. If you are not able to get exact information then you could try those example numbers out and see what you get.

[sentausa]

Ah, I see. Thank you very much.