Forum: Vendor Forum
12-15-2015, 01:04 AM
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Replies: 111
Views: 101,207
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Forum: General
09-22-2015, 12:31 AM
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Replies: 12
Views: 2,822
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Forum: Sample Prep / Library Generation
06-24-2015, 12:21 AM
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Replies: 16
Views: 10,819
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Forum: Epigenetics
05-11-2015, 06:42 AM
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Replies: 3
Views: 3,655
FastQC...
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) has a module that checks for adapter contamination. It looks for the universal adapter sequences (used in TruSeq RNA/DNA and...
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Forum: Sample Prep / Library Generation
05-11-2015, 06:33 AM
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Replies: 23
Views: 20,342
Here a a few tips that I've found through...
Here a a few tips that I've found through experience:
1) titrate your adapter to your sample input. We use 1µL of 15µL for every 500ng of DNA. For making homebrew adapters we follow the protocol in...
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Forum: Vendor Forum
04-30-2015, 03:49 AM
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Replies: 111
Views: 101,207
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Forum: Vendor Forum
04-30-2015, 03:44 AM
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Replies: 111
Views: 101,207
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Forum: Vendor Forum
04-30-2015, 02:37 AM
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Replies: 111
Views: 101,207
I asked the same question to Illumina Tech...
I asked the same question to Illumina Tech Support last week. Here's their response.
"Besides the changes in the software, there was a significant change in the v2 reagents. We changed the dyes of...
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Forum: General
03-30-2015, 11:09 PM
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Replies: 1
Views: 1,702
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Forum: Vendor Forum
12-16-2014, 06:43 AM
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Replies: 111
Views: 101,207
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Forum: Illumina/Solexa
10-29-2014, 07:36 AM
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Replies: 10
Views: 6,585
I'll summarise below
The primers are as...
I'll summarise below
The primers are as follows. I won't put the P5/P7 sequences in here as the are (c) Illumina. You should be able to find them by Googling. Make sure you use the paired end P5 &...
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Forum: Bioinformatics
09-23-2014, 03:01 AM
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Replies: 4
Views: 4,496
I'm using a modified version of a script from...
I'm using a modified version of a script from Shingo Kikugawa
It's single thread, so takes a while. It's still quicker than manual zcatting.
I spoke to Illumina about this and a version of...
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Forum: Illumina/Solexa
08-08-2014, 02:05 AM
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Replies: 37
Views: 46,122
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Forum: Illumina/Solexa
08-07-2014, 08:02 AM
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Replies: 37
Views: 46,122
Your primers are not compatible with the MiSeq....
Your primers are not compatible with the MiSeq. On the HiSeq you can run single read or paired end flow-cells. There are subtle differences between the sequences on the grafted oligos in each flow...
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Forum: Illumina/Solexa
07-16-2014, 01:24 AM
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Replies: 43
Views: 31,879
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Forum: Bioinformatics
06-25-2014, 12:52 AM
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Replies: 4
Views: 4,496
I've spoken to Illumina tech support and they...
I've spoken to Illumina tech support and they have pointed out a possible bug in bcl2fastq v2.
"We identified a bug caused by thread handling that in certain cases caused errors in the order of...
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Forum: Bioinformatics
06-19-2014, 07:11 AM
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Replies: 4
Views: 4,496
Picard failure on NextSeq data
So, we've just begun to run some of our new NextSeq data through our standard pipelines and hit a snag. bcl2fastq still gives us fastq by index, read and lane, so the eight files for every sample are...
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Forum: Illumina/Solexa
06-19-2014, 06:59 AM
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Replies: 1
Views: 4,969
Yep. They've changed the way dual indexing is...
Yep. They've changed the way dual indexing is done on on the NextSeq. BP10 is the primer to read the i5 index and needs to be added to #18 for all dual index runs. Our FAS told us paired end...
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Forum: Bioinformatics
06-04-2014, 06:56 AM
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Replies: 8
Views: 3,394
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Forum: Bioinformatics
06-04-2014, 06:24 AM
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Replies: 8
Views: 3,394
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Forum: Sample Prep / Library Generation
06-02-2014, 02:37 AM
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Replies: 3
Views: 2,088
I was thinking about trying a double...
I was thinking about trying a double normalisation too. First using the Bioanalyser and next by qPCR. Might try that for the next run.
We'll also work on automating qPCR set up to avoid any...
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Forum: Sample Prep / Library Generation
05-30-2014, 07:55 AM
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Replies: 3
Views: 2,088
Inconsitencies with qPCR results
I've begun quantifying all libraries with qPCR (Kapa kit) but I'm getting massive inconsistencies with the number of reads I get from samples in a multiplex pool.
I dilute each final library...
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Forum: Sample Prep / Library Generation
05-30-2014, 02:50 AM
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Replies: 6
Views: 9,447
On a related note, you can also mix and match...
On a related note, you can also mix and match reagents and chips. As long as the protocol you run on the machine matches the reagents you should be gold. You need to load the reagents according to...
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Forum: Vendor Forum
05-22-2014, 04:26 AM
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Replies: 111
Views: 101,207
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Forum: Vendor Forum
05-16-2014, 11:08 AM
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Replies: 111
Views: 101,207
Does this mean you can't do more than 75 cycles...
Does this mean you can't do more than 75 cycles in a 75 cycle kit. I confirmed with tech support that there are 25 additional cycles for dual indexing and we were told we could use those 100 cycles...
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