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Search: Posts Made By: atcghelix
Forum: Bioinformatics 03-07-2017, 08:13 PM
Replies: 21
Views: 7,275
Posted By atcghelix
Are you sure they subtracted the adapter length...

Are you sure they subtracted the adapter length from the fragment sizes to get the insert sizes (meaning, are you sure they're reporting insert size from the bioanalyzer?)? If the fragments...
Forum: MGISEQ (FKA Complete Genomics) 01-27-2017, 05:31 PM
Replies: 5
Views: 6,496
Posted By atcghelix
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...
Forum: Illumina/Solexa 12-04-2016, 11:59 AM
Replies: 6
Views: 1,774
Posted By atcghelix
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...
Forum: Bioinformatics 11-20-2016, 12:42 PM
Replies: 1
Views: 1,788
Posted By atcghelix
Looks like you're trying to trim a FASTA file...

Looks like you're trying to trim a FASTA file (with sequence names starting with >), instead of a FASTQ file (with sequence names starting with @, and 4 lines per sequence):...
Forum: Bioinformatics 11-04-2016, 12:03 PM
Replies: 2
Views: 1,887
Posted By atcghelix
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...
Forum: Bioinformatics 09-14-2016, 02:26 PM
Replies: 4
Views: 1,449
Posted By atcghelix
Of course, something like 100bp SE reads could be...

Of course, something like 100bp SE reads could be an intermediate solution.
Forum: Bioinformatics 09-14-2016, 02:20 PM
Replies: 4
Views: 1,449
Posted By atcghelix
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)...
Forum: Bioinformatics 09-14-2016, 09:43 AM
Replies: 4
Views: 1,449
Posted By atcghelix
Yes it'd be straightforward to downsample to 50bp...

Yes it'd be straightforward to downsample to 50bp reads (for instance, using skewer with the flag "-L 50" to downsample the R1s and just ignore the R2s).

Do you have any expectations regarding the...
Forum: Sample Prep / Library Generation 08-31-2016, 12:11 PM
Replies: 3
Views: 1,231
Posted By atcghelix
We always do that with our libraries and Kapa LTP...

We always do that with our libraries and Kapa LTP library prep kits. You resuspend beads in water then add PEG at specific fractions to wash away small fragments/adapters/dimers/etc...

Essentially...
Forum: Bioinformatics 05-26-2016, 05:35 PM
Replies: 3
Views: 3,506
Posted By atcghelix
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...
Forum: Bioinformatics 04-01-2016, 03:12 PM
Replies: 2
Views: 1,419
Posted By atcghelix
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...
Forum: Illumina/Solexa 08-26-2015, 07:11 AM
Replies: 5
Views: 4,018
Posted By atcghelix
Ah that makes sense. So you want to see some...

Ah that makes sense. So you want to see some evidence of primer peaks after the PCR is finished?
Forum: Illumina/Solexa 08-25-2015, 08:53 PM
Replies: 5
Views: 4,018
Posted By atcghelix
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...
Forum: Illumina/Solexa 08-25-2015, 05:22 PM
Replies: 5
Views: 4,018
Posted By atcghelix
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...
Forum: Bioinformatics 03-21-2015, 08:52 PM
Replies: 2
Views: 1,474
Posted By atcghelix
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...
Forum: Illumina/Solexa 02-14-2015, 07:08 PM
Replies: 27
Views: 5,026
Posted By atcghelix
Do you have access to a qPCR machine? I'd suggest...

Do you have access to a qPCR machine? I'd suggest trying that out to quantify your samples.

http://seqanswers.com/forums/showthread.php?t=6362
Forum: Illumina/Solexa 02-14-2015, 06:51 PM
Replies: 27
Views: 5,026
Posted By atcghelix
How are you quantifying the concentrations of...

How are you quantifying the concentrations of your samples prior to pooling?
Forum: Bioinformatics 01-23-2015, 09:02 PM
Replies: 5
Views: 2,963
Posted By atcghelix
I would try running it in server-client mode: ...

I would try running it in server-client mode:

http://i.animalgenome.org/bioinfo/resources/manuals/exonerate/server.html
Forum: General 01-22-2015, 11:56 AM
Replies: 10
Views: 3,170
Posted By atcghelix
Looks like Rana sylvatica is approximately a 6gb...

Looks like Rana sylvatica is approximately a 6gb genome? The experiment.com page says you're doing HiSeq2000 2x100bp sequencing--is that to increase coverage over the Moleculo? A single HiSeq 2x100...
Forum: Illumina/Solexa 01-19-2015, 11:22 AM
Replies: 4
Views: 4,794
Posted By atcghelix
I think SNPsaurus's point is more important,...

I think SNPsaurus's point is more important, however. You can get by with far fewer distinct adapters by using the combinatorial aspects of a two-index system.
Forum: Illumina/Solexa 01-16-2015, 04:26 PM
Replies: 4
Views: 4,794
Posted By atcghelix
One good reason is to identify barcode swapping...

One good reason is to identify barcode swapping between samples that can happen during PCR:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245947/
Forum: Sanger/Dye Terminator 10-31-2014, 04:14 PM
Replies: 2
Views: 3,665
Posted By atcghelix
Here is one resource that talks about this issue:...

Here is one resource that talks about this issue:
http://www.nature.com/nbt/journal/v27/n11/abs/nbt.1585.html
Forum: Sample Prep / Library Generation 10-14-2014, 03:24 PM
Replies: 2
Views: 1,280
Posted By atcghelix
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...
Forum: Sample Prep / Library Generation 10-03-2014, 10:39 AM
Replies: 7
Views: 1,763
Posted By atcghelix
Is this for human? We've seen similar post-cap...

Is this for human? We've seen similar post-cap post-pcr DNA amounts when doing capture in a large-genome organism (30gb).
Forum: Academic/Non-Profit Jobs 09-22-2014, 01:02 PM
Replies: 0
Views: 1,084
Posted By atcghelix
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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