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Forum: Sample Prep / Library Generation 11-21-2013, 07:17 AM
Replies: 1
Views: 1,231
Posted By chevrm
You could be introducing bubbles/air gaps into...

You could be introducing bubbles/air gaps into the GX chip when aspirating. You want to make sure that the well bottoms are naked for as little time as possible, and immediately filled with the next...
Forum: Bioinformatics 11-11-2013, 10:10 AM
Replies: 11
Views: 7,709
Posted By chevrm
I am experiencing the same issue as Polecat, also...

I am experiencing the same issue as Polecat, also with blastx. Any ideas?
Forum: Metagenomics 11-11-2013, 04:42 AM
Replies: 5
Views: 3,876
Posted By chevrm
I believe (could be wrong) you're looking for -m....

I believe (could be wrong) you're looking for -m. From the man:

-m: interleaved file of paired reads
usage: initPipeline -q -m file.fastq.12 -d projectDir -i 300:500
Forum: Sample Prep / Library Generation 11-02-2013, 10:06 AM
Replies: 5
Views: 8,089
Posted By chevrm
When was the last time you ran the standards? If...

When was the last time you ran the standards? If you're not running them every time then you're pretty susceptible to pipetting errors in your Q-reagent/buffer sln.
Forum: Metagenomics 10-07-2013, 09:32 AM
Replies: 0
Views: 1,151
Posted By chevrm
HUMAnN for non-HMP?

Quick question regarding metabolic pathway analysis:

Is there currently a software package for environmental samples (not related to the human microbiome project) to analyze metabolism similar to...
Forum: Sample Prep / Library Generation 06-21-2013, 06:13 AM
Replies: 1
Views: 3,364
Posted By chevrm
Why not just do it by hand in excel using total...

Why not just do it by hand in excel using total mass?
Forum: Sample Prep / Library Generation 06-19-2013, 10:31 AM
Replies: 2
Views: 6,255
Posted By chevrm
I'd consider a 12000 chip if you're willing to...

I'd consider a 12000 chip if you're willing to burn 1uL...it should be able to visualize anything over 0.5ng/uL
Forum: Sample Prep / Library Generation 06-17-2013, 08:15 AM
Replies: 7
Views: 4,703
Posted By chevrm
I failed to mention that it depends greatly on...

I failed to mention that it depends greatly on what type of plate/tube you're using. In a V-bottom plate, it will take a few minutes longer than a U-bottom because of the more-gradual taper. I...
Forum: Sample Prep / Library Generation 06-17-2013, 06:51 AM
Replies: 7
Views: 4,703
Posted By chevrm
15 minutes is a bit overkill. You don't want...

15 minutes is a bit overkill. You don't want your beads to "crack" when drying, but you don't want them to have residual ethanol either (effects elution). General rule I use is 2-5 minutes, but...
Forum: Sample Prep / Library Generation 05-31-2013, 01:48 PM
Replies: 10
Views: 2,876
Posted By chevrm
How much material are you starting with? Expect...

How much material are you starting with? Expect 80% recovery on EACH cleanup step (on a bad day). Are you eluting off of your columns with warm water/basic Tris?

Enzymatic reagents are...
Forum: Sample Prep / Library Generation 05-20-2013, 12:56 PM
Replies: 3
Views: 2,974
Posted By chevrm
No experience with putting them together but I...

No experience with putting them together but I don't see why not (as long as similar active temps).

Leaving the exo (plas safe) in the sample is fine as long as it's deactivated either by a heat...
Forum: Sample Prep / Library Generation 05-09-2013, 06:36 AM
Replies: 4
Views: 3,545
Posted By chevrm
SPRI bead binding/unbinding has more to do with...

SPRI bead binding/unbinding has more to do with PEG than anything else. An "elution buffer" (water/basic Tris/etc) will elute off of the beads when NOT in the presence of PEG, which is why you...
Forum: Illumina/Solexa 04-05-2013, 06:34 AM
Replies: 5
Views: 4,151
Posted By chevrm
It might be useful for extremely precious samples...

It might be useful for extremely precious samples where very low inputs are required, but doesn't make much of a difference otherwise.
Forum: Bioinformatics 04-05-2013, 06:25 AM
Replies: 8
Views: 43,760
Posted By chevrm
Mate-pairs are wonderful if you're dealing with...

Mate-pairs are wonderful if you're dealing with particularly tricky assemblies, CNVs, or looking for other structural variations (translocs, etc) but may not be worth it if you don't have any of...
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