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Forum: Core Facilities 07-26-2017, 03:10 PM
Replies: 4
Views: 2,533
Posted By captainentropy
To answer my own question I emailed their tech...

To answer my own question I emailed their tech support and got the following in their reply:



Reagent stability is definitely much better than the BA. Of course, for the costs, it all depends...
Forum: Illumina/Solexa 07-21-2017, 01:31 PM
Replies: 13
Views: 3,097
Posted By captainentropy
I had contacted Illumina - and Sigma - about...

I had contacted Illumina - and Sigma - about alternatives. Sigma says there are none. They were completely unhelpful. They literally told me to just search online for alternatives. (Yeah, no s&!t,...
Forum: Illumina/Solexa 07-21-2017, 10:09 AM
Replies: 13
Views: 3,097
Posted By captainentropy
I called Sigma. If you can't order any of the...

I called Sigma. If you can't order any of the ProClin products they won't approve an order for SeqClin since it contains ProClin.

Can't find any alternatives for ProClin other than azide. Anyone...
Forum: Illumina/Solexa 07-19-2017, 12:46 PM
Replies: 13
Views: 3,097
Posted By captainentropy
Yeah, I just encountered the same problem. Here's...

Yeah, I just encountered the same problem. Here's what I was told:



I'm confused because I know of research and core labs that do not do IVD that have been able to order ProClin.
Forum: Core Facilities 07-18-2017, 03:43 PM
Replies: 4
Views: 2,533
Posted By captainentropy
How long can the reagents sit in the machine...

How long can the reagents sit in the machine between runs?

I'm interested in suggesting my group buy a FA. We already have a Bioanalyzer 2100 but the kits are expensive and the gel only is good...
Forum: Illumina/Solexa 03-04-2015, 04:16 PM
Replies: 14
Views: 9,159
Posted By captainentropy
I like the idea that small fragments would be...

I like the idea that small fragments would be denatured, but wouldn't they reanneal? Plus they'd have to probably be at least ~40 bp in length since small fragments should have been removed in the...
Forum: Illumina/Solexa 03-03-2015, 01:14 PM
Replies: 14
Views: 9,159
Posted By captainentropy
Exactly. So we're back to your original question...

Exactly. So we're back to your original question of what the point of the 70 degree step is. But hey, if it works, then that's a problem solved. But I want to know why. hahaha.



Yes, aka stem...
Forum: Illumina/Solexa 03-03-2015, 12:15 PM
Replies: 14
Views: 9,159
Posted By captainentropy
I don't use the RNA-seq kits but are the adapters...

I don't use the RNA-seq kits but are the adapters blunt on one end? It would have to have the A-overhang on one end for the ligation to work.

Nevertheless, I'm glad I found this post. We'll try...
Forum: Sample Prep / Library Generation 02-02-2015, 03:00 PM
Replies: 13
Views: 6,103
Posted By captainentropy
You will probably need to work out the conditions...

You will probably need to work out the conditions for each chromatin sample regardless.

In my experience, settings are rarely "convertible". Even with the same model of sonicator you can get...
Forum: Bioinformatics 08-18-2014, 12:01 PM
Replies: 132
Views: 41,388
Posted By captainentropy
I see. Yes, that makes sense now. My match is at...

I see. Yes, that makes sense now. My match is at the beginning of the read so there's nothing to the left of it (and thus empty).

Thanks!
Forum: Bioinformatics 08-14-2014, 05:23 PM
Replies: 132
Views: 41,388
Posted By captainentropy
Hi mmartin, I'm using the latest version...

Hi mmartin,

I'm using the latest version (1.5) and I noticed the format of the info file doesn't seem to match exactly with the documentation on github...
Forum: Bioinformatics 07-29-2014, 12:34 PM
Replies: 6
Views: 2,086
Posted By captainentropy
No, you don't need Galaxy. What harryzs posted...

No, you don't need Galaxy. What harryzs posted (directly from the ngsplot website) is correct.

I'm using ngsplot and I do not have Galaxy installed on my server.
Forum: Illumina/Solexa 05-19-2014, 04:48 PM
Replies: 10
Views: 4,260
Posted By captainentropy
Once I read this post on core-genomics it began...

Once I read this post on core-genomics it began to make sense to me how it's working
...
Forum: Sample Prep / Library Generation 10-18-2013, 12:32 AM
Replies: 46
Views: 19,033
Posted By captainentropy
cbird, I agree that the beads are the best choice...

cbird, I agree that the beads are the best choice right now. Beckman told me a while back that these (SPRI select) beads have lower lot-to-lot variability. Maybe there's an improvement in formulation...
Forum: Sample Prep / Library Generation 09-22-2013, 02:01 AM
Replies: 2
Views: 1,699
Posted By captainentropy
ES cells are much more difficult to crosslink and...

ES cells are much more difficult to crosslink and sonicate properly. Their chromatin is much more compact. You first need to optimize this. Start by varying the time and temperature of the...
Forum: Sample Prep / Library Generation 05-16-2013, 05:04 PM
Replies: 46
Views: 19,033
Posted By captainentropy
Input into the PCR or the library prep? Using the...

Input into the PCR or the library prep? Using the old-school gel purification method I would lose most of my DNA before the PCR. It was usually barely detectable I started using 25 ng, 50 ng, or more...
Forum: Illumina/Solexa 03-13-2013, 03:28 PM
Replies: 74
Views: 32,190
Posted By captainentropy
He's using both. The 100 bp ladder was what he...

He's using both. The 100 bp ladder was what he was size-selecting (to illustrate the use of the SPRI bead ratios), the 1kb+ ladder is the size marker for the gel.

Take a look again at the text...
Forum: Bioinformatics 02-22-2013, 02:32 PM
Replies: 10
Views: 9,715
Posted By captainentropy
@rlh60 (and for anyone else interested), FWIW,...

@rlh60 (and for anyone else interested), FWIW, I'm trying out your scripts (starting with #2) and when I run it I get this error (YMMV):


Line 48 is:


Correcting that to:


...and it now...
Forum: Bioinformatics 02-20-2013, 12:00 AM
Replies: 11
Views: 8,079
Posted By captainentropy
Thanks dnewkirk :) I always ignore the...

Thanks dnewkirk :)

I always ignore the dates. A question with an answer many months after the OP is still likely to be valuable for someone out there.
Forum: Bioinformatics 02-19-2013, 07:28 PM
Replies: 11
Views: 8,079
Posted By captainentropy
Thanks dnewkirk, could you tell us what would be...

Thanks dnewkirk, could you tell us what would be the advantage to using your perl script would be over an awk command? I'm not criticizing, just wondering. I use an awk command in a shell script to...
Forum: Bioinformatics 02-19-2013, 06:25 PM
Replies: 11
Views: 8,079
Posted By captainentropy
With the H=111 and $H I think arun is just...

With the H=111 and $H I think arun is just setting an awk variable. I'm not sure what use it has actually in this case. The exact same result can be achieved with "...$1,111,$2}..." The 5th column in...
Forum: Bioinformatics 01-30-2013, 01:44 PM
Replies: 5
Views: 746
Posted By captainentropy
Agreed. I'm wondering if since it was developed...

Agreed. I'm wondering if since it was developed and hosted at the University of Michigan it's behind a login wall for security/legal reasons?
Forum: Bioinformatics 01-30-2013, 01:21 PM
Replies: 5
Views: 746
Posted By captainentropy
I also usually use DAVID (and IPA, but that's not...

I also usually use DAVID (and IPA, but that's not free), but since for my work I've found the Panther pathways to be the most helpful, I just go directly to the Panther website.

Here's a new one...
Forum: Sample Prep / Library Generation 01-29-2013, 03:52 PM
Replies: 46
Views: 19,033
Posted By captainentropy
FWIW, Beckman told me once they don't recommend...

FWIW, Beckman told me once they don't recommend using the Ampure XP beads for what we're using them for because the lot-to-lot variability is too great. I don't know about that, they seem to work for...
Forum: Sample Prep / Library Generation 01-29-2013, 03:45 PM
Replies: 46
Views: 19,033
Posted By captainentropy
Yeah, after looking up their "Double-sided SPRI"...

Yeah, after looking up their "Double-sided SPRI" method it looks to be basically the same. I was taught this technique by someone at the JGI. The "improvements" I made were: to dry the beads at RT...
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