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Forum: Bioinformatics 12-13-2017, 09:02 AM
Replies: 1
Views: 1,891
Posted By GERALD
Dragen

When I first heard about Dragen, it sounded interesting but recently Edico has started to make this platform available on AWS, as well as several Bioinformatics-as-a-service platforms, including...
Forum: Clinical Sequencing 09-07-2016, 10:45 AM
Replies: 2
Views: 6,324
Posted By GERALD
Somatic Variant Reporting

Our department is looking for a software solution to support analysis and reporting of somatic cancer variants (currently panels, but eventually exomes). It looks like most of the currently available...
Forum: General 08-10-2015, 10:31 AM
Replies: 0
Views: 1,229
Posted By GERALD
How many human genomes sequenced so far?

Does anyone know this? The best estimate I've been able to get is from this article...
Forum: Bioinformatics 11-08-2012, 03:23 PM
Replies: 0
Views: 1,271
Posted By GERALD
Few Peaks

I am analyzing a ChIP-Seq data set for another lab. The sequencing seems to have gone quite well, with a high depth of coverage (more than 4million mapped reads in each sample), with length of 50bp...
Forum: General 09-28-2011, 03:56 PM
Replies: 1
Views: 1,164
Posted By GERALD
Sequencing Sector Funds

I was wondering if there are any market indexes that deal specifically with sequencing companies (Illumina, Life Technologies, etc.) Does anyone know of any?
Forum: Bioinformatics 09-18-2011, 12:27 AM
Replies: 3
Views: 1,384
Posted By GERALD
Peaks vs. Genes

I just thought I'd check on what people are using to correlate ChIP-Seq peaks vs. Gene locations at this point. I was trying to find a way to do it with Genome Browser. Any ideas?
Forum: Epigenetics 06-28-2011, 07:23 AM
Replies: 5
Views: 5,030
Posted By GERALD
Methylation Analysis

What is the best option for methylation analysis at this point? We would like to analyze methylation in mouse liver samples and are considering all options: bisulfite, MeDIP, MBD sequencing, etc. ...
Forum: RNA Sequencing 04-03-2011, 04:43 PM
Replies: 0
Views: 1,336
Posted By GERALD
deleted deleted

deleted deleted
Forum: Bioinformatics 02-27-2011, 01:10 PM
Replies: 0
Views: 927
Posted By GERALD
bowtie... quest... pinkthing...

Has anyone been using bowtie for mapping, quest for peak calling and pinkthing for genome-wide summary data?

What genome version do you use for this?
Forum: Bioinformatics 02-22-2011, 08:43 AM
Replies: 3
Views: 3,540
Posted By GERALD
Ensembl vs NCBI

Could someone point me in the right direction to find documentation on ENSEMBL genomes vs NCBI genomes? Is ENSEMBL version 59 the same as hg19?
Forum: Bioinformatics 02-14-2011, 03:47 PM
Replies: 82
Views: 31,906
Posted By GERALD
Are we sure this is real? I hope that one or...

Are we sure this is real? I hope that one or more private companies have the foresight to step up to the plate on this. The commercial potential would be enormous. They just have to be big enough...
Forum: Bioinformatics 01-29-2011, 04:19 PM
Replies: 17
Views: 10,242
Posted By GERALD
bareback

Actually, I have tried this myself and found it to be true. I just made a perl script to copy all the files and rename them (called it goatfooler). Then, I ran CASAVA and used another script to...
Forum: Illumina/Solexa 01-28-2011, 06:08 PM
Replies: 3
Views: 2,217
Posted By GERALD
Gaii

So they're just leaving them out on the sidewalks now? Sad...
It's probably better to have it than not, if your lab does a lot of sequencing, but there are some things to keep in mind.

First,...
Forum: Illumina/Solexa 01-19-2011, 08:44 AM
Replies: 74
Views: 49,350
Posted By GERALD
It sounds like the same reagents on a lower...

It sounds like the same reagents on a lower capacity machine. I think many labs would rather not go to the trouble, especially when you consider that the amount of labor is the same. Also, any word...
Forum: Illumina/Solexa 01-18-2011, 01:01 PM
Replies: 3
Views: 3,661
Posted By GERALD
Flowcell

I looked at Illumina's method and it seems like a big pain, especially if you're not Illumina. I bet Illumina wouldn't like it either. Let us know if you're ever successful.
Forum: Illumina/Solexa 01-18-2011, 10:07 AM
Replies: 3
Views: 3,661
Posted By GERALD
It isn't too hard. It's best to just make your...

It isn't too hard. It's best to just make your oligos as similar as possible to Illumina's own. You should probably refer to this earlier thread on how to design the primers and adapters:...
Forum: RNA Sequencing 09-06-2010, 02:15 PM
Replies: 1
Views: 1,821
Posted By GERALD
RNA-Seq to gene expression

What is the fastest way to get from RNA-Seq experiment to gene names and RPKM values? I have analyzed an experiment with Tophat and Cufflinks, but this seems to produce genome locations and FPKM. ...
Forum: Bioinformatics 06-27-2010, 10:07 AM
Replies: 0
Views: 1,812
Posted By GERALD
Bowtie to Illumina Pipeline Conversion

I was wondering if there is a way to convert from Bowtie output to something similar to Illumina Pipeline output files (like sorted.txt, etc.) Is there a utility for this?
Forum: Epigenetics 06-06-2010, 09:07 PM
Replies: 2
Views: 2,505
Posted By GERALD
ChIP-Seq comparisons

I am interested in methadologies for comparing the results of multiple ChIP-Seq studies (i.e. multiple transcription factors, TFs and histone modifications). Does anyone know of good resources for...
Forum: Illumina/Solexa 06-06-2010, 12:41 PM
Replies: 0
Views: 1,421
Posted By GERALD
basecalling

I'm trying to recall bases on a run with goat, using parameters from another basecalling. I've tried it in 1.6.1 and 1.4.0, but in both cases, it seems to recalculate the phasing and prephasing and...
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