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Forum: Illumina/Solexa 11-12-2015, 01:06 PM
Replies: 2
Views: 1,831
Posted By HMorrison
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...
Forum: Oxford Nanopore 09-18-2015, 09:32 AM
Replies: 1
Views: 3,965
Posted By HMorrison
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...
Forum: Illumina/Solexa 07-22-2015, 10:32 AM
Replies: 6
Views: 2,792
Posted By HMorrison
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...
Forum: Illumina/Solexa 07-02-2015, 12:01 PM
Replies: 6
Views: 2,792
Posted By HMorrison
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...
Forum: Illumina/Solexa 07-02-2015, 10:14 AM
Replies: 6
Views: 2,792
Posted By HMorrison
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...
Forum: 454 Pyrosequencing 02-27-2015, 08:17 AM
Replies: 1
Views: 4,028
Posted By HMorrison
Ours is a big paperweight at the moment. Would...

Ours is a big paperweight at the moment. Would love to hear if you come up with a new function (or find a market).
Forum: Bioinformatics 09-08-2014, 12:09 PM
Replies: 7
Views: 1,336
Posted By HMorrison
That won't give them unique deflines, which I...

That won't give them unique deflines, which I think is what he/she is after for input to clustalw. I still can't tell what the problem is, though.
Forum: Bioinformatics 09-08-2014, 11:52 AM
Replies: 9
Views: 3,615
Posted By HMorrison
I do not understand the question. Can you explain...

I do not understand the question. Can you explain further?
Forum: Bioinformatics 07-10-2013, 07:15 AM
Replies: 9
Views: 3,615
Posted By HMorrison
as a one-off solution: sed -e '$!N;s/\n/\t/'...

as a one-off solution:

sed -e '$!N;s/\n/\t/' file1 > col1
sed -e '$!N;s/\n/\t/' file2 | sed -e '$!N;s/\n/\t/' > col2
paste col1 col2 | fmt -5

>seq1
TTTGGATTACAAAGTTATTTAAATCACATGT.......
Forum: Illumina/Solexa 01-29-2013, 09:07 AM
Replies: 4
Views: 2,539
Posted By HMorrison
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.
Forum: Illumina/Solexa 10-16-2012, 05:50 AM
Replies: 4
Views: 3,047
Posted By HMorrison
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...
Forum: 454 Pyrosequencing 10-02-2012, 05:12 AM
Replies: 16
Views: 5,122
Posted By HMorrison
So, did it help? We are still doing it. Current...

So, did it help? We are still doing it. Current work-around is to underload the plate and simply expect to have to do two runs to get the number of reads that we routinely got up until Dec 2011. ...
Forum: 454 Pyrosequencing 09-07-2012, 01:00 PM
Replies: 9
Views: 13,379
Posted By HMorrison
We've finally got a publication out that details...

We've finally got a publication out that details v6v4 Ti amplification and one in press for v3v5. Better than the HMP (single primer) versions.

Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan...
Forum: Ion Torrent 08-21-2012, 05:59 AM
Replies: 18
Views: 9,777
Posted By HMorrison
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...
Forum: Ion Torrent 08-20-2012, 12:15 PM
Replies: 18
Views: 9,777
Posted By HMorrison
I just did. Not finding a protocol, although I...

I just did. Not finding a protocol, although I did find a posting where selection was for 220 (170-220). I am looking for the equivalent of a gel cut. Never mind. I will return to the search...
Forum: Ion Torrent 08-20-2012, 11:24 AM
Replies: 18
Views: 9,777
Posted By HMorrison
Phillip, can you give an example of a...

Phillip, can you give an example of a double-sided Ampure protocol? Thanks,
Hilary
Forum: 454 Pyrosequencing 07-30-2012, 08:53 AM
Replies: 9
Views: 2,809
Posted By HMorrison
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.,...
Forum: 454 Pyrosequencing 07-25-2012, 08:26 AM
Replies: 16
Views: 5,122
Posted By HMorrison
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. ...
Forum: 454 Pyrosequencing 07-25-2012, 08:04 AM
Replies: 9
Views: 2,809
Posted By HMorrison
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...
Forum: 454 Pyrosequencing 07-25-2012, 07:38 AM
Replies: 16
Views: 5,122
Posted By HMorrison
Hi Aniki, We have had some of these problems...

Hi Aniki,

We have had some of these problems as well. We use LibA LV almost exclusively; for tag sequencing of large amplicons. We have elected not to upgrade to FLX+.



Definitely seen...
Forum: Ion Torrent 07-05-2012, 11:05 AM
Replies: 4
Views: 3,180
Posted By HMorrison
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...
Forum: Sample Prep / Library Generation 07-02-2012, 11:01 AM
Replies: 2
Views: 1,836
Posted By HMorrison
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. ...
Forum: 454 Pyrosequencing 06-27-2012, 04:28 AM
Replies: 6
Views: 2,111
Posted By HMorrison
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...
Forum: Ion Torrent 06-27-2012, 04:23 AM
Replies: 4
Views: 3,180
Posted By HMorrison
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.
Forum: Illumina/Solexa 05-24-2012, 06:04 AM
Replies: 32
Views: 25,414
Posted By HMorrison
Yes, although there are two 'lanes' they have to...

Yes, although there are two 'lanes' they have to be the same sample--I think loaded from the same port. Sorry for the delayed response. Have been fighting with the FLX (and about to give it up).
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