SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 146
Search took 0.01 seconds.
Search: Posts Made By: MissDNA
Forum: Ion Torrent 02-14-2014, 08:45 AM
Replies: 2
Views: 3,331
Posted By MissDNA
I got an answer from tech support: PGM...

I got an answer from tech support:

PGM libraries are not compatible with available Proton chemistry due to their size. Proton libraries may have only up to 270 bp.

Size is critical for...
Forum: Ion Torrent 02-14-2014, 08:25 AM
Replies: 2
Views: 3,331
Posted By MissDNA
Sequencing Ion PGM libraries using Ion Proton

Has anyone sucessfully sequenced 200 bp libraries originally constructed for Ion PGM, using Ion Proton.

We have been told by tech support that it was possible and should work well but our...
Forum: Ion Torrent 02-14-2014, 08:12 AM
Replies: 3
Views: 2,996
Posted By MissDNA
I really hope you guys have opted for MiSeq. ...

I really hope you guys have opted for MiSeq.

We have had the Ion Proton for a bit over a year now and so far nothing really good came out of it.

Answering your questions:
It is very easy to...
Forum: 454 Pyrosequencing 07-21-2012, 05:37 AM
Replies: 4
Views: 2,698
Posted By MissDNA
Sequencing results. Short reads, small number of...

Sequencing results. Short reads, small number of reads, small number of passed filter wells...that kinda result that make you (and/or Roche) think there is a problem with that lot of reagents.
Forum: 454 Pyrosequencing 07-20-2012, 03:36 PM
Replies: 4
Views: 2,698
Posted By MissDNA
What kinda results are you getting? We never...

What kinda results are you getting?

We never used Eppendorf plates but our FAS left some in the lab and we were gonna do a comparison soon.
Forum: 454 Pyrosequencing 07-19-2012, 08:06 AM
Replies: 2
Views: 1,423
Posted By MissDNA
I searched on google and I found a doc about...

I searched on google and I found a doc about microwell bioplates where it says pitch is center to center distance between wells. I am waiting our FAS confirmation about it.
Meanwhile he asked me to...
Forum: 454 Pyrosequencing 07-19-2012, 04:55 AM
Replies: 2
Views: 1,423
Posted By MissDNA
PTP device pitch error message

We started a sequencing run yesterday and when we got to the lab this morning there was the following msg on the Run Browser:

http://i78.photobucket.com/albums/j114/alegerber/foto2.jpg
...
Forum: 454 Pyrosequencing 06-20-2012, 04:34 PM
Replies: 10
Views: 2,431
Posted By MissDNA
We had ours replaced once already but our FAS...

We had ours replaced once already but our FAS came to the lab and did it for us. It seemed fairly simple, actually simpler than I thought. Next time I think we will do by ourselves.
Forum: 454 Pyrosequencing 06-14-2012, 05:01 PM
Replies: 7
Views: 2,652
Posted By MissDNA
We have a few runs with low raw wells number that...

We have a few runs with low raw wells number that Roche admitted it was due to a bead recovery lot. Using the same lot we have some good and some bad runs.
Forum: 454 Pyrosequencing 05-17-2012, 11:02 AM
Replies: 3
Views: 1,881
Posted By MissDNA
We have sequenced libraries almost 1 yr old...

We have sequenced libraries almost 1 yr old without a problem. I was having a discussion about library stability with support this past few days. There is no official recommendation about how long an...
Forum: 454 Pyrosequencing 05-11-2012, 11:37 AM
Replies: 23
Views: 4,966
Posted By MissDNA
The max we ever used was like 27% or so because...

The max we ever used was like 27% or so because we are in a hurry. The results were not bad and consistent with what we had obtained before for the same library with lower enrichment.

Other than...
Forum: 454 Pyrosequencing 05-03-2012, 08:47 AM
Replies: 24
Views: 6,122
Posted By MissDNA
You are right, HMorrison. Our FAS had given me...

You are right, HMorrison. Our FAS had given me the info I posted over the phone but he wrote me yesterday saying:

"All lots of Bead Recovery Reagent will be evaluated, and if some lot presents...
Forum: 454 Pyrosequencing 05-02-2012, 05:54 AM
Replies: 8
Views: 2,177
Posted By MissDNA
I would blame the lot then and not the old beads...

I would blame the lot then and not the old beads for your problem.
We observed the same problem in one of our runs. I contacted support and after all they finally admitted that this lot has been...
Forum: 454 Pyrosequencing 05-02-2012, 05:43 AM
Replies: 8
Views: 2,177
Posted By MissDNA
Which lot did you use? There are at least 2 lots...

Which lot did you use? There are at least 2 lots that have been associated with low number of raw wells.

The person who told me to freeze the beads was from the old support group in Penzberg. I...
Forum: 454 Pyrosequencing 04-27-2012, 09:58 AM
Replies: 24
Views: 6,122
Posted By MissDNA
Our FAS told me today that lot 93866020 is under...

Our FAS told me today that lot 93866020 is under quarantine. It seems obvious some boxes are fine but some have problems. The run we did usinf beads recovered with this lot and that showed low number...
Forum: 454 Pyrosequencing 04-26-2012, 05:41 PM
Replies: 24
Views: 6,122
Posted By MissDNA
We did another run with beads enriched using lot...

We did another run with beads enriched using lot 9386020. We got over 1,6 million reads even though we had a problem while assembling the run: the tech forgot to incubate the beads with DBIM, she...
Forum: 454 Pyrosequencing 04-26-2012, 05:33 PM
Replies: 8
Views: 2,177
Posted By MissDNA
One time we were having problems with our machine...

One time we were having problems with our machine and could not sequence. We had already enriched some beads, support recommended we should freeze the beads and thaw only for sequencing. I donīt...
Forum: 454 Pyrosequencing 04-26-2012, 05:30 PM
Replies: 8
Views: 5,118
Posted By MissDNA
What is usually the percentage of true PE reads...

What is usually the percentage of true PE reads in a 20 kb prep?
Iīve done several 3 kb preps but never 8 or 20 kb. I believe in our 3 kb preps we get 50.60% of true PE reads.
Forum: 454 Pyrosequencing 04-20-2012, 01:13 PM
Replies: 24
Views: 6,122
Posted By MissDNA
As I mentioned on my earlier post I had the...

As I mentioned on my earlier post I had the problem you described for this lot. I submitted the case yesterday. I was told by Roche people that I should not realy on forum info. However if was not...
Forum: 454 Pyrosequencing 04-19-2012, 04:50 AM
Replies: 24
Views: 6,122
Posted By MissDNA
FAS told me the lot was not flagged. We did the...

FAS told me the lot was not flagged. We did the sequencing run and what was noticiable was a very low raw well number, which made me remember a post I saw on this forum:

"93852420 we had problems...
Forum: 454 Pyrosequencing 04-17-2012, 11:07 AM
Replies: 17
Views: 4,035
Posted By MissDNA
Yeah, we do the same. One of our clients really...

Yeah, we do the same. One of our clients really wanted SG processing but in the end when he started working with the data, he realized that eventhough there was a lot more reads with SG processing,...
Forum: 454 Pyrosequencing 04-17-2012, 11:04 AM
Replies: 17
Views: 4,035
Posted By MissDNA
900 k reads is a pretty good result for amplicon...

900 k reads is a pretty good result for amplicon processing, which is expected to give up 30% less data than SG. Which data set are you going to work with?
Forum: 454 Pyrosequencing 04-17-2012, 10:58 AM
Replies: 24
Views: 6,122
Posted By MissDNA
We did a LV recovery today using lot 93866020 for...

We did a LV recovery today using lot 93866020 for the first time. It was necessary 12 washes while normally we do around 6-7. At the end we got around 2.5 million beads per cup, which is perfect for...
Forum: 454 Pyrosequencing 04-17-2012, 10:55 AM
Replies: 17
Views: 4,035
Posted By MissDNA
What kind of data do you get when using amplicon...

What kind of data do you get when using amplicon pipeline for analysis?
I am not a bioinformatician and understand very little about processing but our bioinoformatician would always use amplicon...
Forum: 454 Pyrosequencing 04-13-2012, 08:32 AM
Replies: 24
Views: 6,122
Posted By MissDNA
Roche is going to replace all our 93848420 and...

Roche is going to replace all our 93848420 and 93852420 boxes. They said we should discard all the 8420 boxes but we should save the boxes from 2420 that present normal quantity of beads to be used...
Showing results 1 to 25 of 146

 


All times are GMT -8. The time now is 08:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO