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Forum: Illumina/Solexa 09-17-2015, 03:25 PM
Replies: 3
Views: 1,123
Posted By cnicolet
Thank you! Sorry for lateness, was expecting...

Thank you! Sorry for lateness, was expecting email notification after responses
Forum: Illumina/Solexa 08-25-2015, 10:58 AM
Replies: 3
Views: 1,123
Posted By cnicolet
ATAC PE vs SR

Has anyone compared ATAC run as PE vs SR? Everyone requests PE but why is that more necessary than, for example, with ChIP or FAIRE?
Forum: Illumina/Solexa 02-27-2015, 09:13 AM
Replies: 2
Views: 1,938
Posted By cnicolet
sorry for the late response, I used to get emails...

sorry for the late response, I used to get emails when someone answered the post. I don't have specific before and after because the several runs before the super wash were abysmal, since the wash...
Forum: Illumina/Solexa 02-19-2015, 12:50 PM
Replies: 2
Views: 1,938
Posted By cnicolet
Nextseq500 Super Wash

Ask your FAS's about the super wash protocol for NextSeqs, it is not part of the normal maintenance and I haven't seen much written on it yet. But it worked wonders on our NextSeq when we were...
Forum: Bioinformatics 09-22-2014, 02:45 PM
Replies: 4
Views: 3,950
Posted By cnicolet
nextseq bcl2fastq

this is a little off topic from the thread but seems related to some of the things both you guys are doing--do you have a slick way to zcat the bcl2fastq output correctly? I've been doing it "by...
Forum: Illumina/Solexa 02-20-2014, 10:57 AM
Replies: 4
Views: 2,346
Posted By cnicolet
Thanks for your comments. That is an excellent...

Thanks for your comments. That is an excellent point, I'm sure we are feeding all known exons so that could be a big part of it. I'll know a lot more when we send the sureselect material info...
Forum: Illumina/Solexa 02-19-2014, 08:57 AM
Replies: 4
Views: 2,346
Posted By cnicolet
Nextera exome kit

Hi:
Recently we tested the nextera exome enrichment libe kit. In our analysis pipeline we have a metric that calculates exonic reads, intronic reads, and intergenic reads. Our nextera libes all...
Forum: Academic/Non-Profit Jobs 07-02-2013, 02:58 PM
Replies: 0
Views: 1,144
Posted By cnicolet
Genomics Job Opportunity at USC

The Dornsife College of Letters, Arts, and Sciences at the University of Southern California is seeking an individual to direct the Genomics Core Facility. The Genomics Core provides...
Forum: Bioinformatics 10-22-2012, 08:26 AM
Replies: 0
Views: 1,090
Posted By cnicolet
bam to sgr

Anyone have a good way to convert a bam to an sgr? Thanks!
Forum: Illumina/Solexa 08-02-2012, 02:33 PM
Replies: 10
Views: 6,779
Posted By cnicolet
Thanks for the info! We primarily do WGBS but...

Thanks for the info! We primarily do WGBS but had a customer with RRBS (love acronyms). We have had other tech issues with WGBS though and I would be grateful if we could initiate a dialog and...
Forum: Illumina/Solexa 07-31-2012, 08:10 AM
Replies: 10
Views: 6,779
Posted By cnicolet
Thanks for the info, your experiece mirrors ours....

Thanks for the info, your experiece mirrors ours. I was hoping someone had good tricks to fool the computer/software. We have done these runs on the GA using the prescribed settings and it worked...
Forum: Illumina/Solexa 07-30-2012, 04:10 PM
Replies: 10
Views: 6,779
Posted By cnicolet
The adapters in Illumina DNA sample prep kits are...

The adapters in Illumina DNA sample prep kits are methylated, so can be used for bar-coded bisulfite libes. We have made many of these. The only downside is the oligos are expensive since we...
Forum: Illumina/Solexa 05-22-2012, 07:53 AM
Replies: 3
Views: 2,076
Posted By cnicolet
Thanks for the advice! Side by side comparison...

Thanks for the advice! Side by side comparison with Pfu shows no differences, but contacting Kapa tech support is a good idea. Methylation levels among the different libraries have not been...
Forum: Illumina/Solexa 05-21-2012, 10:48 AM
Replies: 3
Views: 2,076
Posted By cnicolet
Bisulfite sequencing bias

Hello all:

We have been having a bias problem on our whole genome bisulfite libraries, very severe dropouts in CpG islands. Coverage across the rest of the genome is very good. We are using the...
Forum: Illumina/Solexa 12-09-2011, 03:21 PM
Replies: 5
Views: 5,121
Posted By cnicolet
Thanks Simon! We did find some info on that...

Thanks Simon! We did find some info on that using the --fastq-cluster-count parameter. But it's a little confusing, the manual says "Specify 0 to ensure creation of a single FASTQ file" then later...
Forum: Illumina/Solexa 12-08-2011, 09:41 AM
Replies: 5
Views: 5,121
Posted By cnicolet
Casava1.8.2

Hi:
How are people feeling about CASAVA 1.8.2? We are just starting to use it and so far are underwhelmed. The new formats are cumbersome and the way it delivers multiple files is complicating...
Forum: Illumina/Solexa 11-16-2011, 02:56 PM
Replies: 27
Views: 9,789
Posted By cnicolet
We have done several runs mixing different index...

We have done several runs mixing different index primers into the existing illumina index read mix (HP8), sometimes with the nextera indexing primers and sometimes with different custom primers. The...
Forum: Illumina/Solexa 10-13-2011, 08:50 AM
Replies: 10
Views: 4,276
Posted By cnicolet
Thanks Phillip, this is very helpful. I have...

Thanks Phillip, this is very helpful. I have been getting good advice from you since my days running a Sanger sequencing core!
Forum: Illumina/Solexa 10-12-2011, 12:02 PM
Replies: 3
Views: 3,176
Posted By cnicolet
Is this plant RNA? You won't get a good RIN from...

Is this plant RNA? You won't get a good RIN from that, but it looks intact.
Forum: Illumina/Solexa 10-12-2011, 11:38 AM
Replies: 10
Views: 4,276
Posted By cnicolet
Cluster gradient

We routinely see similar gradients, and see it regardless of the cBot we use (we have two). I think this is just a reflection of reagent flow, as noted in an earlier thread. The cluster station...
Forum: Illumina/Solexa 04-19-2011, 12:58 PM
Replies: 27
Views: 9,789
Posted By cnicolet
single lane multiplexing

also, we found out that HP7 has the indexing and the regular read 2 primer in it (that is, HP7 will work on plain old non-truseq PE libraries). While HP7 is not available to order as stand-alone (of...
Forum: Illumina/Solexa 11-16-2010, 01:06 PM
Replies: 3
Views: 2,968
Posted By cnicolet
CBot vs. Cluster station

Hello:
Illumina says the cBot will give slightly higher cluster numbers than the cluster station with the same library concentration. Has anyone seen this? How much higher? We are using 10 pM...
Forum: Bioinformatics 09-27-2010, 10:04 AM
Replies: 5
Views: 6,404
Posted By cnicolet
An investigator on the UCD campus thought that's...

An investigator on the UCD campus thought that's what they were doing at BGI, and he's changed over the way his lab is doing things, plus telling everyone else about it. So to my mind there is zero...
Forum: Bioinformatics 09-27-2010, 09:35 AM
Replies: 5
Views: 6,404
Posted By cnicolet
Library complexity

Hi:
We have been told that illumina gDNA libraries prepared by standard protocols are less complex than believed, and that essentially you max out on the information content with limited numbers...
Forum: Illumina/Solexa 05-11-2010, 10:50 AM
Replies: 18
Views: 6,315
Posted By cnicolet
We had been using the bioanalyzer, 90% of the...

We had been using the bioanalyzer, 90% of the time it is right on ("right on" for us is 6-7 pM) but the other 10% has been too much to deal with. We've lately been using the KAPA biosystems qPCR...
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