Forum: Bioinformatics
03-07-2017, 09:13 PM
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Replies: 21
Views: 7,899
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Forum: MGISEQ (FKA Complete Genomics)
01-27-2017, 06:31 PM
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Replies: 5
Views: 7,201
Do you often find that restriction enzyme...
Do you often find that restriction enzyme inhibitors are a problem nucacidhunter? We sometimes have samples that drastically don't behave like others in their group and I've been wondering how often...
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Forum: Illumina/Solexa
12-04-2016, 12:59 PM
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Replies: 6
Views: 1,850
I agree that using inline barcodes is often...
I agree that using inline barcodes is often inconvenient, and you do have to be careful about color balancing if you design them yourself. Also, keep in mind that you lose bases off of your R1/R2 if...
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Forum: Bioinformatics
11-20-2016, 01:42 PM
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Replies: 1
Views: 1,880
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Forum: Bioinformatics
11-04-2016, 01:03 PM
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Replies: 2
Views: 2,106
The samtools "depth" command should output the...
The samtools "depth" command should output the coverage at only the bases that have a depth of at least 1 if that's what you want.
But this is conceptually different than filtering out repetitive...
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Forum: Bioinformatics
09-14-2016, 03:26 PM
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Replies: 4
Views: 1,518
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Forum: Bioinformatics
09-14-2016, 03:20 PM
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Replies: 4
Views: 1,518
Your expectations for polymorphism will likely...
Your expectations for polymorphism will likely depend on the spatial scale of your study. We found that roughly 70% of our RAD loci contained at least one variable site (and 30% were invariant)...
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Forum: Bioinformatics
09-14-2016, 10:43 AM
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Replies: 4
Views: 1,518
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Forum: Sample Prep / Library Generation
08-31-2016, 01:11 PM
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Replies: 3
Views: 1,311
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Forum: Bioinformatics
05-26-2016, 06:35 PM
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Replies: 3
Views: 3,751
It can apparently be helpful for things like...
It can apparently be helpful for things like ancient DNA extractions where the percentage of exogenous DNA is high.
This is the paper I know of, and they have instructions of making the baits...
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Forum: Bioinformatics
04-01-2016, 04:12 PM
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Replies: 2
Views: 1,500
Hi David,
Flagstat just counts the SAM...
Hi David,
Flagstat just counts the SAM flags, so if you haven't marked reads as duplicates (generally through a tool such as picard MarkDuplicates), then you won't see any.
Whether or not you...
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Forum: Illumina/Solexa
08-26-2015, 08:11 AM
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Replies: 5
Views: 4,366
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Forum: Illumina/Solexa
08-25-2015, 09:53 PM
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Replies: 5
Views: 4,366
Thanks for the feedback. Starting template was...
Thanks for the feedback. Starting template was quantified using a quant-it dsDNA assay kit (broad range) (http://www.thermofisher.com/order/catalog/product/Q33130) on a PerkinElmer Victor plate...
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Forum: Illumina/Solexa
08-25-2015, 06:22 PM
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Replies: 5
Views: 4,366
High-weight bioanalyzer fragments after PCR
Hi Everyone,
We've been doing a dual-SPRI size selection prior to library prep to try to restrict our fragments to 200-500bp (hoping to sequence PE 100bp on a HiSeq 3000). After this size...
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Forum: Bioinformatics
03-21-2015, 09:52 PM
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Replies: 2
Views: 1,569
If you're talking about unique with regards to...
If you're talking about unique with regards to mapping positions on both ends, how about marking duplicates using Picard's MarkDuplicates tool, then using samtools flagstat? You can subtract the...
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Forum: Illumina/Solexa
02-14-2015, 08:08 PM
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Replies: 27
Views: 5,149
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Forum: Illumina/Solexa
02-14-2015, 07:51 PM
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Replies: 27
Views: 5,149
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Forum: Bioinformatics
01-23-2015, 10:02 PM
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Replies: 5
Views: 3,182
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Forum: General
01-22-2015, 12:56 PM
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Replies: 10
Views: 3,391
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Forum: Illumina/Solexa
01-19-2015, 12:22 PM
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Replies: 4
Views: 5,305
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Forum: Illumina/Solexa
01-16-2015, 05:26 PM
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Replies: 4
Views: 5,305
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Forum: Sanger/Dye Terminator
10-31-2014, 05:14 PM
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Replies: 2
Views: 3,801
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Forum: Sample Prep / Library Generation
10-14-2014, 04:24 PM
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Replies: 2
Views: 1,395
Stretching Kapa library preps
Hi Everyone,
Has anyone tried doing half reactions with the Kapa library prep kits using 1000ng of input DNA? I'm curious if the amount of reagents in a half-reaction is enough to ligate adapters...
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Forum: Sample Prep / Library Generation
10-03-2014, 11:39 AM
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Replies: 7
Views: 1,900
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Forum: Academic/Non-Profit Jobs
09-22-2014, 02:02 PM
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Replies: 0
Views: 1,176
Postdoctoral Scholar:Population Genomics
The Shaffer Lab at UCLA (https://www.eeb.ucla.edu/Faculty/Shaffer/) is recruiting a postdoctoral scholar to join our team. The primary goals for this postdoc are to work with our lab on several...
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