SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 12 of 12
Search took 0.01 seconds.
Search: Posts Made By: Calluna
Forum: Illumina/Solexa 07-22-2014, 07:12 AM
Replies: 2
Views: 1,891
Posted By Calluna
My initial thought is that there may not have...

My initial thought is that there may not have been enough diversity across reads. What was your indexing scheme? Did you follow the indexing guidelines in the Nextera XT sample prep guide?

See...
Forum: Illumina/Solexa 03-11-2014, 09:50 AM
Replies: 3
Views: 1,585
Posted By Calluna
I have not yet tried half reactions, but this...

I have not yet tried half reactions, but this (http://seqanswers.com/forums/showthread.php?t=41259) post might be helpful. Things you've probably already considered... I would also imagine that...
Forum: Illumina/Solexa 08-01-2013, 01:01 PM
Replies: 7
Views: 8,844
Posted By Calluna
I haven't tried it for mixed length indices, but...

I haven't tried it for mixed length indices, but I have done it for a run of dual and single index samples. In that case, you can make the sample sheet for a dual index run and use the adapter...
Forum: Sample Prep / Library Generation 07-18-2013, 07:20 AM
Replies: 12
Views: 6,844
Posted By Calluna
I'm glad your Q scores and PF improved. The...

I'm glad your Q scores and PF improved. The first thing that comes to mind is to ask how you determined concentration of your libraries. If it was based off High Sensitivity BA, I get quite a bit...
Forum: Illumina/Solexa 07-17-2013, 01:34 PM
Replies: 2
Views: 1,668
Posted By Calluna
Here are a couple of links that should help: ...

Here are a couple of links that should help:

http://res.illumina.com/documents/products/technotes/technote_coverage_calculation.pdf

http://www.illumina.com/CoverageCalculator
Forum: Sample Prep / Library Generation 07-17-2013, 09:13 AM
Replies: 12
Views: 6,844
Posted By Calluna
I'm not sure how crucial it is to have your...

I'm not sure how crucial it is to have your denature NaOH concentration at at least 0.1N, so I wouldn't mess with it if you don't have to.

This is what I would suggest instead:

Denature:
5uL...
Forum: Sample Prep / Library Generation 07-17-2013, 07:09 AM
Replies: 3
Views: 2,667
Posted By Calluna
I've used the NEB Single Cell WGA kit to extract...

I've used the NEB Single Cell WGA kit to extract and amp <10 cells. It's expensive, but seems to work well.

https://www.neb.com/products/e2620-single-cell-wga-kit#tabselect0
Forum: Sample Prep / Library Generation 07-10-2013, 08:07 AM
Replies: 12
Views: 6,844
Posted By Calluna
Call Illumina and ask if 0.1N NaOH will be strong...

Call Illumina and ask if 0.1N NaOH will be strong enough.

If not, you can use a higher concentration NaOH, but less of it... and then neutralize.

I think you can do the following (but double...
Forum: Illumina/Solexa 07-10-2013, 07:42 AM
Replies: 30
Views: 25,597
Posted By Calluna
abyss, For our samples I think it might be...

abyss,

For our samples I think it might be something with the libraries themselves. We ran the same samples (new pools) on the Hi-Seq wtih much more PhiX (i.e. ~30-50%); they again clustered low....
Forum: Sample Prep / Library Generation 07-05-2013, 08:33 AM
Replies: 12
Views: 6,844
Posted By Calluna
I forgot to mention, if your libraries are not...

I forgot to mention, if your libraries are not very diverse, I would also recommend spiking in some PhiX. If you have the updated Miseq software, I believe you can get by with 5% for very low...
Forum: Sample Prep / Library Generation 07-05-2013, 08:31 AM
Replies: 12
Views: 6,844
Posted By Calluna
I may have done my math incorrectly, but I came...

I may have done my math incorrectly, but I came up with a final NaOH concentration of 0.002N in your final mixture. If so, that would probably explain the low cluster density/low passing filter. ...
Forum: Illumina/Solexa 06-27-2013, 12:20 PM
Replies: 30
Views: 25,597
Posted By Calluna
Hi abyss, I've been having some issues with...

Hi abyss,

I've been having some issues with cluster density lately, and was wondering if you've had any luck figuring out the cause of your low-clustering samples.

Briefly, I'm running some...
Showing results 1 to 12 of 12

 


All times are GMT -8. The time now is 12:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO