LongTrace question

[Muz]

Hi, I’m interested in trying your “LongTrace” trace reprocessing service and I’m wondering how it will handle re-sequencing projects that consist of template derived from PCR products. At the moment we are using primer sets that generate short amplicons, is there any reason why we couldn’t produce bigger amplicons and use this service to achieve longer runs?

[Daniel]

None at all. This is in fact the best way to make use of LongTrace – change your set up to make best of the increase in read length.

If you haven’t already tried the free service then give it try. The only thing to watch for is make sure that the traces you use are long enough for LongTrace to actually make a difference – there is no point processing 500bp PCR fragments because the trace signal ends before the normal resolution of the sequencer is reached (ie the signal is already as good as it could be before longtrace processing).

Daniel Tillett
Nucleics Support

[Muz]

Thanks, I’ll give it a try. How long does it take to get the results back? I actually have a large set of .ab1 files in our archive from a BAC sequencing project undertaken a couple of years ago. We are coming under pressure to keep the .scf files and let the .ab1 files go. Unfortunately there was not sufficient coverage to align these into long contigs and I was wondering if I submitted them for long trace processing do you think this would help with the alignment? It would be nice to finish this project without doing more physical sequencing. On this note can LongTrace use .scf files as an input?

[Daniel]

Usually you will get your traces back in under a minute – it depends a bit on how many traces you have uploaded and how many other people are using the server.

Reprocessing traces from incomplete BAC assemblies works really well. We did a study earlier in the year looking at exactly this. Just by re-processing we were able to turn BACs that couldn’t be assembled into single contigs. If you want to try LongTrace on a BACs worth of traces send me a PM or email me and I will arrange for a large scale trial.

Finally, don’t throw out your ab1 traces! The reason that they are bigger than the scfs is they contain the raw trace data. It is by reprocessing the raw data that LongTrace can get longer reads.

Cheers

Daniel Tillett
Nucleics Support

[Muz]

Thanks. I will keep my abi files.

[Author]

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