454 paired-end or single-end?

[ps376]

Hi,

We have recently received 454 targeted sequencing data, and I am having trouble finding if the data is paired-end or single-end. Where can I find this information? I am looking to detect copy number variation from the reads, and therefore need to know if I should be using the pairs or split-read info.

The original targets were enriched using one sequence capture array. The raw data reads reported fall in two regions (even though there are 4 samples, each has a separate MID tag). Do these two 'regions' correspond to different pairs?

Thank you!

[maven]

They aren't paired. You can verify this by assembling the data with the 454 assembler - if it was paired, the assembler will tell you this. But because it's SeqCap i guarantee it's not paired. The 2 regions correspond to the 2 physical regions of the PTP - there are 2 independent flow cells on each run and they each get their own data file.

[Muraya]

I am not sure how you are estimating your CNV, I would guess assembly is done computational and highly similar sequence will typically collapse into one unit and this will definitely result in underestimation of the copy number of the sequences