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Search: Posts Made By: der_eiskern
Forum: General 10-01-2014, 07:47 AM
Replies: 9
Views: 5,970
Posted By der_eiskern
Good to know! so you do use the AATI (not...

Good to know!

so you do use the AATI (not Agilent) for quantitation?
Forum: General 09-30-2014, 09:44 AM
Replies: 9
Views: 5,970
Posted By der_eiskern
re:

i'm very concerned about AATI's inability to provide specs for their DNA quantitation abilities. Is it still recommended to use picogreen for library quantitation and only use microcapillaries for...
Forum: Sample Prep / Library Generation 08-18-2010, 08:56 AM
Replies: 49
Views: 61,598
Posted By der_eiskern
AmpureXP binding capacity?

Anyone know about the ampure XP binding capacity for the beads? other magnetic bead systems claim 2 micrograms per 100 micrograms of beads.

Thanks,
Der.
Forum: Genomic Resequencing 04-03-2010, 01:40 PM
Replies: 4
Views: 2,821
Posted By der_eiskern
many of the NGS companies have protocols for such...

many of the NGS companies have protocols for such small quantities of isolated nucleic acid. i'd call your favorites and ask tech support to ask R&D.

one strategy you might want to consider is to...
Forum: Illumina/Solexa 03-05-2010, 12:33 PM
Replies: 20
Views: 4,889
Posted By der_eiskern
is it your impression that this decrease in...

is it your impression that this decrease in quality and "PF flattening out" is a optics problem or a software problem? I'm wondering how far the user community feels that they can push their current...
Forum: Sample Prep / Library Generation 02-24-2010, 02:26 PM
Replies: 13
Views: 16,995
Posted By der_eiskern
illumina may recommend smaller library sizes but...

illumina may recommend smaller library sizes but i'm pretty sure there are people using 1kb or 2kb insert sizes in parallel with the 200-700 bp sizes for structural variant discovery.
Forum: Illumina/Solexa 02-10-2010, 09:31 PM
Replies: 10
Views: 8,354
Posted By der_eiskern
it appears the Sanger Institute has been...

it appears the Sanger Institute has been performing ssRNA-seq (http://www.ncbi.nlm.nih.gov/pubmed/19609351) (published July 2009)
Forum: Illumina/Solexa 02-10-2010, 06:28 PM
Replies: 43
Views: 131,335
Posted By der_eiskern
Have you figured out what went wrong yet? I just...

Have you figured out what went wrong yet? I just read your post and had some thoughts.



hrm...what side of the adaptors were truncated? were the truncations always from the 5' end or 3' end?...
Forum: Bioinformatics 02-09-2010, 09:13 PM
Replies: 9
Views: 4,946
Posted By der_eiskern
perhaps in the next release the error report...

perhaps in the next release the error report could look a little bit more like this :)
Forum: Illumina/Solexa 02-04-2010, 11:23 AM
Replies: 145
Views: 289,792
Posted By der_eiskern
i can say the SE adaptors worked on my GAIIx SE...

i can say the SE adaptors worked on my GAIIx SE sequencing runs last August with the latest kits at the time.
Forum: Illumina/Solexa 12-14-2009, 12:41 PM
Replies: 18
Views: 5,155
Posted By der_eiskern
4 pM was too little for our GAIIx machine. 8 pM...

4 pM was too little for our GAIIx machine. 8 pM gave us the so-called "sweet spot" in the 180,000-220,000 clusters/tile range.

i've compared all those but Qubit, which is just a fluorimeter,...
Forum: Illumina/Solexa 12-14-2009, 11:54 AM
Replies: 18
Views: 5,155
Posted By der_eiskern
i've tested the bioanalyzer versus QPCR for...

i've tested the bioanalyzer versus QPCR for quantifying the library and they're roughly equivalent in my hands.
Forum: Illumina/Solexa 12-11-2009, 04:05 PM
Replies: 8
Views: 4,212
Posted By der_eiskern
i'm not sure what exactly you want ("an average...

i'm not sure what exactly you want ("an average for those passing-filter reads")

but i've also noticed often two-thirds of the 30-10% of unmappable reads are alignable if you can tolerate a higher...
Forum: Illumina/Solexa 12-11-2009, 03:56 PM
Replies: 9
Views: 3,281
Posted By der_eiskern
if i recall correctly we've noticed higher error...

if i recall correctly we've noticed higher error rates in the second read and attributed it to the lower signal-to-background ratio. i hear that PE constraints on mapping help make up for this...
Forum: Illumina/Solexa 12-11-2009, 03:51 PM
Replies: 0
Views: 1,529
Posted By der_eiskern
Lightbulb error rate

has anyone attempted to use a program like novoalign to better estimate the actual error rate of illumina sequencing protocol? i saw some discussion here...
Forum: Bioinformatics 12-11-2009, 02:41 PM
Replies: 4
Views: 5,590
Posted By der_eiskern
Lightbulb SE novoaligned data to MAQ pileup?

So I aligned my Single-End illumina data with MAQ then took all the unmappable reads and aligned those with NovoAlign. Now I'm wondering if I should use the novo2maq function and combine the novo.map...
Forum: Illumina/Solexa 11-05-2009, 03:39 PM
Replies: 11
Views: 8,323
Posted By der_eiskern
advantT, greigite posted a great resource on this...

advantT, greigite posted a great resource on this topic (see the pdf here (http://seqanswers.com/forums/showpost.php?p=4493&postcount=26)):...
Forum: Illumina/Solexa 10-20-2009, 05:43 PM
Replies: 11
Views: 8,323
Posted By der_eiskern
we've noticed a dramatic improvement of our...

we've noticed a dramatic improvement of our library generation when using "homemade" phosphorothioate primers (like the Nature paper) compared to unmodified oligos.
Forum: Bioinformatics 10-20-2009, 05:41 PM
Replies: 6
Views: 3,510
Posted By der_eiskern
novoalign and bfast appear to be quite similar to...

novoalign and bfast appear to be quite similar to me. nils, care to comment on the differences?
Forum: General 10-20-2009, 05:35 PM
Replies: 3
Views: 4,551
Posted By der_eiskern
James, is your 24M current best from a single...

James, is your 24M current best from a single lane before or after passing filter? Just want to make sure I'm not comparing apples and oranges (i got between 20 and 27M before filtering with on...
Forum: Illumina/Solexa 10-20-2009, 05:20 PM
Replies: 2
Views: 3,176
Posted By der_eiskern
Is the flowcell's layout known to affect perceived cluster density on a given tile?

I just did my first sequencing run on the GAIIx. I was doing some quality control calculations from the data contained in the Summary File and I noticed something that I didnt' expect to see.

i...
Forum: Bioinformatics 09-29-2009, 01:19 PM
Replies: 21
Views: 30,478
Posted By der_eiskern
I heard bowtie is great for mapping Chromatin IPs...

I heard bowtie is great for mapping Chromatin IPs and RNA back to a reference but isn't as good as MAQ for finding snps though. Is this accurate?
Forum: Illumina/Solexa 09-21-2009, 03:35 PM
Replies: 18
Views: 5,155
Posted By der_eiskern
rune, Any idea how wide the variation they say...

rune, Any idea how wide the variation they say there is?

we haven't run enough samples on our GA2x to know it that well yet.
Forum: Illumina/Solexa 09-18-2009, 05:40 PM
Replies: 5
Views: 4,563
Posted By der_eiskern
Hi I'm interested in the metric of relating...

Hi I'm interested in the metric of relating cluster density to % use-able sequences after built-in QC functions are run on the machine itself. I've heard stories of people getting great cluster...
Forum: Illumina/Solexa 09-18-2009, 05:31 PM
Replies: 18
Views: 5,155
Posted By der_eiskern
how much are you loading these days? i've heard...

how much are you loading these days? i've heard of some people having to load 48 picomolar gDNA for PE Seq.

I'm also trying to figure out how much Illumina says you SHOULD be having to load to get...
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