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Forum: Ion Torrent 10-03-2011, 01:28 PM
Replies: 7
Views: 3,841
Posted By wildung
Sorry for the late replies. Details to run:...

Sorry for the late replies.

Details to run: Build the PCR master mix with five pipettings, make sure two reagents are full, push go. Really not that much more than add new collections tubes and...
Forum: Ion Torrent 09-27-2011, 07:55 AM
Replies: 7
Views: 3,841
Posted By wildung
OneTouch impression

We've had our PGM since December '10 and were one of the first to sign up to buy a onetouch last winter. We were lucky enough to be a test case to see if we could intall it and run it ourselves...
Forum: Bioinformatics 09-27-2011, 07:36 AM
Replies: 8
Views: 1,850
Posted By wildung
or there is this shell script in the manual. ...

or there is this shell script in the manual.
from the assemblydirectory:

fgrep Singleton 454ReadStatus.txt > singles.txt
sfffile -o singles.sff -i singles.txt your/path/to/the.sff
sffinfo -s...
Forum: Ion Torrent 06-02-2011, 10:26 AM
Replies: 10
Views: 4,156
Posted By wildung
Which is it?: Your enrichment level is too high...

Which is it?: Your enrichment level is too high if you are able to enrich 70-80% of the total beads, then either there is too much library going into the emPCR or your emulsions are breaking, OR is...
Forum: Ion Torrent 03-12-2011, 10:33 AM
Replies: 14
Views: 11,294
Posted By wildung
I would be shocked if ABI didn't jump on the...

I would be shocked if ABI didn't jump on the automation problem before the transaction was complete. As for posting, I usually don't. I can't post too much because I really enjoy being this old and...
Forum: Ion Torrent 03-11-2011, 05:05 PM
Replies: 14
Views: 11,294
Posted By wildung
oops

consensus accuracy was 99.1% on a 5Mb genome.
Forum: Ion Torrent 03-11-2011, 04:25 PM
Replies: 14
Views: 11,294
Posted By wildung
144k reads, 14.9Mb newbler says 77% Q40+ by...

144k reads, 14.9Mb newbler says 77% Q40+ by consensus accuracy. >99% of my reads mapped to the refn. Not bad out of the block. Bet the next improvement in signal processing is will take the Q up to...
Forum: Ion Torrent 03-11-2011, 01:24 PM
Replies: 14
Views: 11,294
Posted By wildung
My $0.02

Got 15Mb out of the 10Mb chip 1st time out of the box and cut a ridiculous number of corners in the protocol. From breaking emPCR to starting the seqn run can be an easy one person day. Still would...
Forum: Ion Torrent 03-07-2011, 04:24 PM
Replies: 14
Views: 11,294
Posted By wildung
Test fragments ran fine. Playing with our first...

Test fragments ran fine. Playing with our first libraries, now. Lots of people said it was all hype and asked why would anyone buy a 10Mb instrument. This is why. It always looked to me like it...
Forum: 454 Pyrosequencing 11-19-2010, 04:39 PM
Replies: 11
Views: 3,165
Posted By wildung
Roche says the new oil should have a clear layer...

Roche says the new oil should have a clear layer on top of the reaction after the run. That means I now find it impossible to tell if an emulsion is broken. With the old oil I tossed 3 or more...
Forum: 454 Pyrosequencing 11-19-2010, 04:31 PM
Replies: 13
Views: 3,631
Posted By wildung
By the time I'm satisfied with the quality of my...

By the time I'm satisfied with the quality of my mRNA I rarely have >1.0% yield. The Rapid cDNA Library calls for 200ng starting material, so 20ug should get you in the ballpark. I usually ask for...
Forum: 454 Pyrosequencing 11-19-2010, 04:26 PM
Replies: 13
Views: 3,631
Posted By wildung
By the time I'm satisfied with the quality of my...

By the time I'm satisfied with the quality of my mRNA I rarely have >1.0% yield. The Rapid cDNA Library calls for 200ng starting material, so 20ug should get you in the ballpark. I usually ask for...
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