Forum: Illumina/Solexa
09-21-2020, 08:17 AM
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Replies: 1
Views: 1,234
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Forum: Bioinformatics
03-11-2020, 05:55 AM
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Replies: 5
Views: 1,174
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Forum: Bioinformatics
03-10-2020, 12:20 PM
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Replies: 5
Views: 1,174
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Forum: Bioinformatics
03-09-2020, 11:38 AM
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Replies: 5
Views: 1,174
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Forum: Illumina/Solexa
02-27-2020, 09:01 AM
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Replies: 3
Views: 1,492
mdegraaf,
You didn't say how many libraries...
mdegraaf,
You didn't say how many libraries you pooled. If it is more than 12 then it is inevitable that you have more than one library sharing a common i7 index sequence. i7 is the first of the...
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Forum: Bioinformatics
02-13-2020, 09:45 AM
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Replies: 2
Views: 1,212
Sometimes the old solutions are the best...
Sometimes the old solutions are the best solutions, the good ol' Unix join command:
join -e 'NNNNNNNNNNNNNNNNNNNNNNNN' -1 1 -2 1 -a 1 -a 2 -o '0,1.2,2.2' Input1.txt Input2.txt
Assumptions
...
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Forum: Sample Prep / Library Generation
11-22-2019, 12:59 PM
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Replies: 4
Views: 2,025
What I am saying is that for those 5 lanes I...
What I am saying is that for those 5 lanes I mentioned there are 2 very closely spaced peaks, one labeled as a peak of ~1,260-1,270bp and the peak just after that labeled as the Upper marker. The...
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Forum: Sample Prep / Library Generation
11-22-2019, 09:47 AM
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Replies: 4
Views: 2,025
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Forum: Sample Prep / Library Generation
11-07-2019, 07:33 AM
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Replies: 2
Views: 1,551
Don't over interpret the differences between...
Don't over interpret the differences between these two traces since they were obviously performed using different instruments. The one on the left appears to be an Advanced Analytical Fragment...
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Forum: Sample Prep / Library Generation
10-16-2019, 09:06 AM
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Replies: 6
Views: 2,529
LV,
Your description sounds very familiar....
LV,
Your description sounds very familiar. Our core went through much the same with our Fragment Analyzer: unexplained failures followed by perfect runs, repeated communication with Tech Support...
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Forum: Illumina/Solexa
10-10-2019, 05:25 AM
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Replies: 2
Views: 1,836
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Forum: Bioinformatics
09-18-2019, 06:53 AM
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Replies: 9
Views: 3,270
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Forum: Sample Prep / Library Generation
09-18-2019, 05:56 AM
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Replies: 21
Views: 8,424
According to Illumina...
According to Illumina (https://www.illumina.com/products/selection-tools/rrna-depletion-selection-guide.html) they have a new product pending for bacteria and plant leaf tissues. They state to...
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Forum: Sample Prep / Library Generation
08-02-2019, 08:37 AM
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Replies: 2
Views: 1,863
Are you sure that it really is low cluster...
Are you sure that it really is low cluster density? Do you have access to the Thumbnails? When a flow cell is very overloaded it may falsely report a low cluster density. I ask because our experience...
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Forum: Illumina/Solexa
05-31-2019, 08:48 AM
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Replies: 14
Views: 4,270
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Forum: Illumina/Solexa
05-10-2019, 05:00 AM
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Replies: 5
Views: 1,982
Yes, Illumina sequencers absolutely require...
Yes, Illumina sequencers absolutely require sequencing and index read* primers. Bridge amplification and sequence generation are separate things. Every Illumina reagent kit/cartridge has tubes/wells...
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Forum: Illumina/Solexa
05-09-2019, 02:36 PM
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Replies: 5
Views: 1,982
The custom sequencing and index primers are...
The custom sequencing and index primers are complementary to the target specific portions of the original PCR primers, plus the pad and linker. For example, if the amplicon you are sequencing is...
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Forum: Illumina/Solexa
05-09-2019, 05:35 AM
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Replies: 5
Views: 1,982
It sounds like your new lab is following the...
It sounds like your new lab is following the protocol developed by Patrick Schloss' lab (or something very similar) for construction dual indexed Illumina amplicon libraries. You can review the full...
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Forum: Oxford Nanopore
05-09-2019, 05:27 AM
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Replies: 6
Views: 7,619
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Forum: Illumina/Solexa
05-09-2019, 05:02 AM
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Replies: 2
Views: 1,669
Phillip,
Our lab does essentially the same...
Phillip,
Our lab does essentially the same as you, remove solution from cartridge, mix in Eppendorf, return to cartridge, but they use disposable Pasteur pipets to suck the sample out of and...
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Forum: Illumina/Solexa
04-18-2019, 07:06 AM
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Replies: 3
Views: 2,385
Julia,
Pardon what may be a stupid question...
Julia,
Pardon what may be a stupid question but how did you get the run started without a sample sheet? The MiSeq requires a sample sheet matching the reagent cartridge name and if it can't find...
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Forum: General
04-03-2019, 02:12 PM
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Replies: 2
Views: 3,651
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Forum: General
02-20-2019, 07:29 AM
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Replies: 15
Views: 10,081
Hello all. It has been a while since Illumina...
Hello all. It has been a while since Illumina BaseSpace ClarityLIMS (nee Genologics) has been discussed and I wanted to see how users are feeling about the direction of the product since Illumina has...
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Forum: Illumina/Solexa
11-26-2018, 12:59 PM
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Replies: 7
Views: 2,790
In my opinion it is unwise to install software...
In my opinion it is unwise to install software patches which have not been tested for compatibility by Illumina. We do not patch any instrument computers with anything other than patches/upgrades...
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Forum: Bioinformatics
11-14-2018, 05:35 AM
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Replies: 4
Views: 1,694
frymor,
You correctly identified the cause...
frymor,
You correctly identified the cause in your last statement above. The Illumina NextSeq500 (and NovaSeq) use 2 Color Chemistry for tagging and identifying bases. Using this system G's are...
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