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Search: Posts Made By: anjama
Forum: General 02-20-2019, 06:02 AM
Replies: 5
Views: 599
Posted By anjama
It sounds something like this:...

It sounds something like this: https://www.thermofisher.com/order/catalog/product/403081

From your description, I don't think that's the one you're looking for, but the terms there might get you...
Forum: Sample Prep / Library Generation 02-20-2019, 05:45 AM
Replies: 0
Views: 320
Posted By anjama
Agilent SureSelect XT and Illumina flowcell saturation

Does anyone know if the SureSelect XT kits have enough probes in a single reaction to saturate a single lane in an Illumina HiSeq flowcell (200-400 million reads) with unique fragments? My concern is...
Forum: Sample Prep / Library Generation 05-17-2018, 02:41 PM
Replies: 1
Views: 584
Posted By anjama
CTAB alternative for carboxyl mag bead gDNA extraction

Last summer I developed a protocol for our lab to extract gDNA from tissue samples using the carboxyl coated magnetic beads used in SPRI. It has worked really well with a lot of advantages including...
Forum: Sample Prep / Library Generation 04-03-2018, 06:09 AM
Replies: 1
Views: 575
Posted By anjama
Why would ligation fail with different isoschizomer?

We're having a weird issue with trying to ligate Illumina adapters to DNA extracted from cattle egrets (a bird species). Doesn't matter if the DNA is extracted from blood or tissue. Initially, when...
Forum: Sample Prep / Library Generation 07-02-2017, 06:07 PM
Replies: 3
Views: 1,619
Posted By anjama
Thanks for the input. Based on input here and...

Thanks for the input. Based on input here and experimenting in the lab, it looks like we'll be incorporating replication into our Picogreen protocol to ensure good consistency.
Forum: Sample Prep / Library Generation 07-02-2017, 05:59 PM
Replies: 3
Views: 1,049
Posted By anjama
Optimizing magnetic bead mix for gDNA extraction

I've been working with the protocol in this thread for making magnetic bead mixes: http://seqanswers.com/forums/showthread.php?t=49507

I have it working well as a substitute for Ampure/SPRIselect,...
Forum: Sample Prep / Library Generation 06-08-2017, 04:49 PM
Replies: 3
Views: 1,619
Posted By anjama
qubit and picogreen discrepancies

We're a small lab that has done most of our quantitation using nanodrop and qubit, depending on the application. However, as we try to prepare multiplexed illumina libraries for dsDNA, we're trying...
Forum: Sample Prep / Library Generation 06-05-2017, 06:30 AM
Replies: 12
Views: 6,320
Posted By anjama
I actually just came across this thread trying to...

I actually just came across this thread trying to figure what is clumping my beads, but in my case I was using them to extract dna from digested tissue in lysis buffer. Based on your comment and the...
Forum: Sample Prep / Library Generation 05-12-2017, 04:42 PM
Replies: 2
Views: 971
Posted By anjama
For the species I'm working with it'll probably...

For the species I'm working with it'll probably be single-end, but other people might do short paired-end reads where they overlap

I have some ligation products left over from our last titration...
Forum: Sample Prep / Library Generation 05-11-2017, 03:54 PM
Replies: 2
Views: 971
Posted By anjama
GBS: eliminating adpater contamination in library for Illumina platform

We're in the process of trying to create our own GBS libraries for various species. The step we're having the most trouble with right now is optimizing the adapter concentration to avoid having...
Forum: General 03-10-2017, 10:02 AM
Replies: 1
Views: 1,550
Posted By anjama
PstI methylation sensitivity

So my lab is in the process of understanding and implementing a protocol for several species. One point of confusion we are trying to figure out is whether or not the PstI restriction enzyme is...
Forum: Pacific Biosciences 09-16-2016, 12:24 PM
Replies: 5
Views: 2,192
Posted By anjama
Okay, I generated a loading report. The first row...

Okay, I generated a loading report. The first row is the species from which we got typical results. The second row is the first attempt at the problematic species. The third row is the second...
Forum: Pacific Biosciences 09-16-2016, 06:21 AM
Replies: 5
Views: 2,192
Posted By anjama
I don't see anything a report called a loading...

I don't see anything a report called a loading report, or that gives p0, p1, p2 statistics. I've attached screenshots of the reports I do have. The left side is the problematic species. The right...
Forum: Pacific Biosciences 09-14-2016, 09:15 AM
Replies: 5
Views: 2,192
Posted By anjama
Low read counts from old PacBio data

I've been helping other people with processing PacBio data using the SMRTanalysis software. Basically, for our purposes, I've just been using the reads of insert protocol. This has worked great for...
Forum: Pacific Biosciences 03-31-2016, 10:16 AM
Replies: 1
Views: 1,504
Posted By anjama
Developing microsatellites from pacbio reads

Disclaimer: everything I know about Pacbio has been learned over the process of the last few days. I'm basically the closest thing to a bioinformatician in our lab, so I'm helping some people figure...
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