Forum: Illumina/Solexa
11-12-2015, 01:06 PM
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Replies: 2
Views: 2,040
Non-random Illumina sequencing error?
We have observed a couple of relatively frequent (1:4) SNPs in what is supposed to be a clonal culture. The simplest explanation is that it's not a clonal culture, but has anyone ever observed what...
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Forum: Oxford Nanopore
09-18-2015, 09:32 AM
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Replies: 1
Views: 4,652
Input DNA requirement for MinION
Would someone who's been using the MinION through MAP tell me what the input DNA starting amount should be? There's size selection possibly both before and after shearing with associated loss, so...
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Forum: Illumina/Solexa
07-22-2015, 10:32 AM
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Replies: 6
Views: 3,431
NextSeq500 early results
James,
I am very pleased with our early results. I spent a lot of time looking at quality scores and accuracy (based on phix, which was the only control we used). The only quality drop off...
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Forum: Illumina/Solexa
07-02-2015, 12:01 PM
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Replies: 6
Views: 3,431
Thanks for the quick answers. I looked at the...
Thanks for the quick answers. I looked at the earlier thread, but didn't find much regarding quality. I think the adapter trimming crept in because of the new format of the SampleSheet.csv. The...
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Forum: Illumina/Solexa
07-02-2015, 10:14 AM
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Replies: 6
Views: 3,431
NextSeq500 early results
Hi all,
We replaced our Hiseq1000 with a NextSeq, largely due to the expense of the HS maintenance contract and the long run time. Our installation and training runs seemed fine, and I'm trying...
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Forum: 454 Pyrosequencing
02-27-2015, 08:17 AM
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Replies: 1
Views: 4,253
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Forum: Bioinformatics
09-08-2014, 12:09 PM
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Replies: 7
Views: 1,514
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Forum: Bioinformatics
09-08-2014, 11:52 AM
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Replies: 9
Views: 4,156
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Forum: Bioinformatics
07-10-2013, 07:15 AM
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Replies: 9
Views: 4,156
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Forum: Illumina/Solexa
01-29-2013, 09:07 AM
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Replies: 4
Views: 2,753
Service contract costs
Has anyone bought a service contract on either Miseq or Hiseq1000 yet? If so, what was the cost? I have projected the usual 10% of acquisition cost.
Thanks for any info.
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Forum: Illumina/Solexa
10-16-2012, 05:50 AM
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Replies: 4
Views: 3,242
Warning--more than just the first four bases of...
Warning--more than just the first four bases of read one are critical, but not for cluster finding. We tried the game of putting four random bases at the start of read 1 based on what we knew about...
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Forum: 454 Pyrosequencing
10-02-2012, 05:12 AM
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Replies: 16
Views: 5,402
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Forum: 454 Pyrosequencing
09-07-2012, 01:00 PM
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Replies: 9
Views: 13,895
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Forum: Ion Torrent
08-21-2012, 05:59 AM
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Replies: 18
Views: 10,494
Thanks so much, Eric. We'll experiment with MW...
Thanks so much, Eric. We'll experiment with MW ladder and try to add it to the repertoire. In fact, we'd like to eliminate very large fragments as well as the ones under 300. Standard Ampure clean...
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Forum: Ion Torrent
08-20-2012, 12:15 PM
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Replies: 18
Views: 10,494
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Forum: Ion Torrent
08-20-2012, 11:24 AM
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Replies: 18
Views: 10,494
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Forum: 454 Pyrosequencing
07-30-2012, 08:53 AM
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Replies: 9
Views: 3,002
v9 primers
We have used
1510R, CCTTCYGCAGGTTCACCTAC
with a combination of
1380F CCCTGCCHTTTGTACACAC
1389F TTGTACACACCGCCC
Citation is Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L. A.,...
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Forum: 454 Pyrosequencing
07-25-2012, 08:26 AM
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Replies: 16
Views: 5,402
pre-annealing enrichment primer
Hi,
This is the protocol (developed by Sharon Grim, who uses this forum but doesn't post often):
Combine 12.5 ul enrichment primer, 80 ul washed enrichment beads, 900 ul enhancing fluid. ...
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Forum: 454 Pyrosequencing
07-25-2012, 08:04 AM
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Replies: 9
Views: 3,002
v9 on Illumina vs. GSFLX
rRNA amplicon sequencing is 90% of what we do; we used 454 because that's what was available to do 'long' reads back in 2005. Recall that the original Solexa reads were 35 nt. We're shifting 18s v9...
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Forum: 454 Pyrosequencing
07-25-2012, 07:38 AM
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Replies: 16
Views: 5,402
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Forum: Ion Torrent
07-05-2012, 11:05 AM
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Replies: 4
Views: 3,390
Update
We wanted to use it for ribosomal RNA amplicon analysis (or other molecular marker analysis by amplicon sequencing). It has too high an error rate for this purpose and is too expensive and labor...
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Forum: Sample Prep / Library Generation
07-02-2012, 11:01 AM
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Replies: 2
Views: 2,229
96 well PCR clean up
Anyone found a 96 well clean up method that will remove 100 nt/bp and smaller from ~250 bp product? Most give 100 bp as the cutoff, but we've gotten too much small material back with Qiaquick 96. ...
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Forum: 454 Pyrosequencing
06-27-2012, 04:28 AM
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Replies: 6
Views: 2,260
no easy solution
We did this by mistake a while ago (March 2011)--after trying various ways to get the information ourselves, had to send the run files to GS Support where they were able to get the two datasets...
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Forum: Ion Torrent
06-27-2012, 04:23 AM
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Replies: 4
Views: 3,390
OneTouch and ES available
PGM users:
We have a OneTouch and ES (also Guava, preconfigured Qubit2, and various reagents and supplies) for sale; any reasonable offer considered. Have decided to cut our losses with the PGM.
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Forum: Illumina/Solexa
05-24-2012, 06:04 AM
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Replies: 32
Views: 26,593
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