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Forum: Bioinformatics 12-07-2014, 04:24 AM
Replies: 1
Views: 710
Posted By singlemoleculer
Helicos imaging

Here is the short version of Helicos imaging from Current Protocols in Molecular Biology, supplement 92, 7.10.10. This was published in 2010 and, alas, nothing has changed since then.
During a...
Forum: General 02-25-2014, 04:32 PM
Replies: 10
Views: 1,850
Posted By singlemoleculer
I can't comment on the T issue. No clue either....

I can't comment on the T issue. No clue either. As for more than 5 bases, there are hordes of different modified bases that vary with species. In humans 5meC is most common but that is not true for...
Forum: General 02-25-2014, 10:52 AM
Replies: 10
Views: 1,850
Posted By singlemoleculer
I think you are referring to the Oxford data that...

I think you are referring to the Oxford data that was discussed but not really shown at AGBT12. At AGBT14, more detail was given though still limited. Average read length in the data described by...
Forum: General 02-25-2014, 10:12 AM
Replies: 10
Views: 1,850
Posted By singlemoleculer
One advantage to nanodetector technologies like...

One advantage to nanodetector technologies like Oxford and Nabsys is that they are single molecule so you look at individual molecules rather than large pools of identical molecules. Typically, you...
Forum: Helicos / Direct Genomics 10-24-2012, 03:56 PM
Replies: 1
Views: 3,108
Posted By singlemoleculer
If you want to look at transcriptome data, both...

If you want to look at transcriptome data, both tag and RNA-seq, go to http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0019287

From that paper: "Transcript counts for all...
Forum: Helicos / Direct Genomics 09-19-2012, 03:55 AM
Replies: 18
Views: 9,072
Posted By singlemoleculer
The standard Helicos filtering software gets rid...

The standard Helicos filtering software gets rid of these artifacts automatically. If you don't have access to the software, you can do manual filtering. Very rich in AT means A+T>90%. These are...
Forum: Helicos / Direct Genomics 08-24-2012, 11:16 AM
Replies: 18
Views: 9,072
Posted By singlemoleculer
Dolphin22- Your low aligned yield rate could be...

Dolphin22-
Your low aligned yield rate could be caused by many things but you can frequently diagnose some of the problems by looking at the sequence of what doesn't align. If they are very rich in...
Forum: The Pipeline 02-21-2012, 09:04 AM
Replies: 103
Views: 135,244
Posted By singlemoleculer
Deletion rate of 17%

Based on Oxford Nanopore's press release (http://www.nanoporetech.com/news/press-releases/view/39) and their spelling of lambda, looks like they are trying to prepare us for lots of deletions.
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