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Forum: 454 Pyrosequencing 01-10-2012, 10:26 AM
Replies: 7
Views: 3,304
Posted By vamosia
my suspicions is that using -large will cause the...

my suspicions is that using -large will cause the algorithm to take shortcuts and not completely traverse the entire contigGraph (since well its too large). It may so happen that the missing contigs...
Forum: 454 Pyrosequencing 01-10-2012, 10:22 AM
Replies: 5
Views: 8,905
Posted By vamosia
Yes its possible, you can ignore the MID section....

Yes its possible, you can ignore the MID section. But you'll need to specify your primers (forward and reverse) as well as what your reference sequences are.
Forum: 454 Pyrosequencing 01-10-2012, 10:18 AM
Replies: 12
Views: 6,697
Posted By vamosia
As far as know 454 does not provide...

As far as know 454 does not provide unidirectional amplicon sequencing. So for now you're stuck with sequencing both direction. (You can theoretically use the Lib-L shotgun protocol to perform a...
Forum: 454 Pyrosequencing 01-10-2012, 10:16 AM
Replies: 7
Views: 4,657
Posted By vamosia
You'll need to combined all the primer into one...

You'll need to combined all the primer into one file. i.e

cat primers1.fasta primers2.fasta > primers.fasta

then used the combined primer file

runAssembly -o name -vt primers.fasta *.sff...
Forum: Bioinformatics 12-06-2011, 06:11 AM
Replies: 3
Views: 4,325
Posted By vamosia
I would suggest primer_match. It is rather simple...

I would suggest primer_match. It is rather simple to use and rather flexible in its output.

The primers in this specific case would be your 20bp sequence. The program would in turn allow you to...
Forum: Bioinformatics 12-06-2011, 06:06 AM
Replies: 2
Views: 1,903
Posted By vamosia
Have you checked the 454AllStructVars.txt? One...

Have you checked the 454AllStructVars.txt? One possibility is that there wasn't enough confidence in that that particular "deleted" region to classify it as "High Confidence".

Such variations...
Forum: 454 Pyrosequencing 11-29-2011, 05:43 PM
Replies: 2
Views: 1,621
Posted By vamosia
Last time i install one, the installation GUI has...

Last time i install one, the installation GUI has an option to specify if you what to install it at a local directory. Is this still not the case? at any rate you can actually just move the files...
Forum: Bioinformatics 11-29-2011, 05:38 PM
Replies: 12
Views: 21,646
Posted By vamosia
There is a roche script called "sffinfo", which...

There is a roche script called "sffinfo", which takes and sff file and generate a fasta file.
Forum: Bioinformatics 11-29-2011, 05:32 PM
Replies: 18
Views: 6,583
Posted By vamosia
It seems to me that your depth is too high. Since...

It seems to me that your depth is too high. Since errors accumulate, the more depth means more chances of introducing errors, hence breaking the assembly. I would suggest try lowing the depth and see...
Forum: Core Facilities 10-18-2011, 08:10 AM
Replies: 8
Views: 6,004
Posted By vamosia
On my previous microbes projects, 20X seems to be...

On my previous microbes projects, 20X seems to be the depth that works well with Newbler. More depth will typically break the contig more since the errors accumulate and less depth does not generate...
Forum: 454 Pyrosequencing 10-18-2011, 08:01 AM
Replies: 3
Views: 2,123
Posted By vamosia
As far as I know, prior to assembly, newbler will...

As far as I know, prior to assembly, newbler will trim the reads back using its own set of separate parameter. So the trimmed reads (by newbler) are used as the input for the algorithm.

So in...
Forum: Bioinformatics 10-13-2011, 11:40 AM
Replies: 3
Views: 4,033
Posted By vamosia
IGV (http://www.broadinstitute.org/igv/) should...

IGV (http://www.broadinstitute.org/igv/) should give you something similar.

It doesn't quite annotate the genome, but it will give you corresponding information where annotation information is...
Forum: 454 Pyrosequencing 10-11-2011, 09:59 AM
Replies: 6
Views: 2,166
Posted By vamosia
Great, keep in mind that the amplicon pipeline...

Great, keep in mind that the amplicon pipeline does several additional correction to help reduce homopolymer error (amplicon library are generally very bright, hence more chance of producing...
Forum: 454 Pyrosequencing 10-11-2011, 09:54 AM
Replies: 1
Views: 1,551
Posted By vamosia
You'll mostly likely need to play around with the...

You'll mostly likely need to play around with the parameters to see what best work for you data, but in my case the 90% identity and 80% query coverage (-mi 90% -ml 80%) gives the best results for my...
Forum: 454 Pyrosequencing 10-11-2011, 09:10 AM
Replies: 6
Views: 2,166
Posted By vamosia
Which pipeline are you using? The ends of the...

Which pipeline are you using? The ends of the reads may be of lower quality, which may caused reads to be filtered out.

If your still interested in the those rejected reads anyway, you could try...
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