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Forum: Ion Torrent 05-20-2015, 09:52 PM
Replies: 2
Views: 2,576
Posted By maven
One barcode because Ion Torrent software doesn't...

One barcode because Ion Torrent software doesn't look for barcodes on the other ends.
Forum: 454 Pyrosequencing 07-03-2012, 10:26 AM
Replies: 13
Views: 10,134
Posted By maven
Hi Sven, Does that really work? I was under the...

Hi Sven,
Does that really work? I was under the impression that the /bin/sh dependency is failing because there is no entry for it in the (perhaps non-existent on Ubuntu) rpm database, not because a...
Forum: 454 Pyrosequencing 03-06-2012, 02:40 AM
Replies: 14
Views: 2,000
Posted By maven
Whether or not shotgun or amplicon is more...

Whether or not shotgun or amplicon is more appropriate for 16S has a lot to do with how diverse your 16S sample happens to be. Maybe yours isn't that diverse, and so isn't that shotgun-like.
Forum: 454 Pyrosequencing 01-11-2012, 11:12 AM
Replies: 5
Views: 8,905
Posted By maven
Himalaya, you are right - totally on me for...

Himalaya, you are right - totally on me for providing misinformation. However as you've discovered, you will still have to configure the MID in AVA and use a multiplexer because the MID is still in...
Forum: 454 Pyrosequencing 01-11-2012, 03:28 AM
Replies: 5
Views: 8,905
Posted By maven
If your original sff file has MIDs, why are you...

If your original sff file has MIDs, why are you splitting them ahead of time? You should leave them alone and demultiplex in AVA. Besides, when you split using sffinfo, you get fasta files not sff...
Forum: 454 Pyrosequencing 11-02-2011, 05:30 AM
Replies: 6
Views: 3,077
Posted By maven
It's impossible to completely turn off the...

It's impossible to completely turn off the filters. The pipeline is built so that quality filtering is not optional. Each individual filter may or may not be completely bypassed. At the basecalling...
Forum: 454 Pyrosequencing 10-13-2011, 03:17 PM
Replies: 2
Views: 5,006
Posted By maven
They aren't paired. You can verify this by...

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...
Forum: 454 Pyrosequencing 08-15-2011, 07:46 AM
Replies: 1
Views: 2,445
Posted By maven
Take it to your support rep. Newbler's genome...

Take it to your support rep. Newbler's genome size estimate are calculated directly from the coverage depth histogram immediately preceding it in the 454NewblerMetrics.txt file. So if that histogram...
Forum: Bioinformatics 02-22-2010, 08:09 AM
Replies: 8
Views: 6,015
Posted By maven
-noa is supposed to tell it to not actually...

-noa is supposed to tell it to not actually bother doing the assembly itself. The -no option turns off most output generation, since the goal here is to just generate the split fasta (and qual) file....
Forum: Bioinformatics 02-22-2010, 06:53 AM
Replies: 8
Views: 6,015
Posted By maven
This can be done with 454 software too, although...

This can be done with 454 software too, although there are bound to be differences in the result based on the specifics of the linker-recognition algorithms.

runAssembly -tr -noa -no myfile.sff
...
Forum: Bioinformatics 10-15-2009, 06:46 AM
Replies: 19
Views: 6,530
Posted By maven
As far as I know, the mapper won't automatically...

As far as I know, the mapper won't automatically offset coordinates in the snp file to reflect the subsequence you used in your mapping. You should extract the SNPs from the regions of interest from...
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