SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 79
Search took 0.01 seconds.
Search: Posts Made By: strob
Forum: Bioinformatics 06-30-2014, 09:38 PM
Replies: 3
Views: 2,578
Posted By strob
Dear all, I want to re-open this discussion...

Dear all,

I want to re-open this discussion as I have a similar question: how can I detect and extract overhanging reads, and this at both ends of my reference?
I have overlapping MiSeq reads...
Forum: Bioinformatics 04-25-2012, 05:05 AM
Replies: 4
Views: 1,712
Posted By strob
I used two different methods to extract my DNA,...

I used two different methods to extract my DNA, which was than sequenced and assembled. I want now to know which method gave me the best results, by comparing the two assemblies. I want to find out...
Forum: Bioinformatics 04-24-2012, 10:25 PM
Replies: 4
Views: 1,712
Posted By strob
How two compare two assembly results? (not assembly tools)

Hi,

most of the time, people compare results, using the same dataset, but obtained from different tools (example: velvet vs. soapdenovo)

I have however two independent datasets (solexa data,...
Forum: Bioinformatics 10-07-2011, 01:25 AM
Replies: 9
Views: 2,937
Posted By strob
could be of interest to read before starting a...

could be of interest to read before starting a new experiment:

Genome Biology 2011, 12:125 doi:10.1186/gb-2011-12-8-125
Published: 25 August 2011

The real cost of sequencing: higher than you...
Forum: The Pipeline 08-23-2011, 11:07 PM
Replies: 0
Views: 2,979
Posted By strob
NHGRI funds development of revolutionary DNA sequencing technologies

http://www.genome.gov/27545118

Bethesda, Md., Mon., Aug. 22, 2011 Researchers today received more than $14 million in grants to develop DNA sequencing technologies that will rapidly sequence a...
Forum: Literature Watch 07-17-2011, 10:09 PM
Replies: 2
Views: 2,050
Posted By strob
Comparative studies of de novo assembly tools for next-generation sequencing technolo

Comparative studies of de novo assembly tools for next-generation sequencing technologies

http://bioinformatics.oxfordjournals.org/content/27/15/2031.full.pdf+html
Forum: Bioinformatics 07-12-2011, 05:42 AM
Replies: 1
Views: 1,270
Posted By strob
Assembly Comparison

Dear all,

Let's say I have performed several assemblies on the same dataset and I would like to compare the results. I know I can look at N50, average contig length, etc. But I was more thinking...
Forum: Events / Conferences 05-02-2011, 01:37 AM
Replies: 0
Views: 2,380
Posted By strob
Workshop on Cutting-edge Bioinformatics - BGI

Workshop on Cutting-edge Bioinformatics

June 20-24, 2011, Shenzhen, China

Workshop on Cutting-edge Bioinformatics will be organized by BGI (formerly known as the Beijing Genomics Institute),...
Forum: The Pipeline 01-03-2011, 11:50 PM
Replies: 8
Views: 10,331
Posted By strob
Maybe these can be added to this already existing...

Maybe these can be added to this already existing list: http://seqanswers.com/forums/showthread.php?t=4229
Forum: Literature Watch 10-19-2010, 03:31 AM
Replies: 0
Views: 1,949
Posted By strob
Comparing de novo assemblers for 454 transcriptome data

Comparing de novo assemblers for 454 transcriptome data
Sujai Kumar and Mark L Blaxter

BMC Genomics 2010, 11:571doi:10.1186/1471-2164-11-571

Published: 16 October 2010
Abstract...
Forum: Bioinformatics 10-07-2010, 05:29 AM
Replies: 7
Views: 2,994
Posted By strob
highly repetitive.... we have the illumina...

highly repetitive....
we have the illumina dataset available. But we are thinking of adding a 454 low coverage set. I think we can do three things:
- all de novo (hybrid assembly)
- illumina de...
Forum: Bioinformatics 10-07-2010, 03:54 AM
Replies: 7
Views: 2,994
Posted By strob
low 454 coverage combined with high solexa coverage

Hi,

has anybody experience with combining following two datasets:

1X coverage of 454 reads (backbone)
30X coverage of solexa reads

background: we are talking about a non sequenced plant...
Forum: General 08-11-2010, 10:33 PM
Replies: 8
Views: 3,020
Posted By strob
Hi, if you sequence your data with BGI, the...

Hi,

if you sequence your data with BGI, the bioinformatics analysis are included. And from our experience they are not only with many people, they also provide really nice curated data (even on...
Forum: Bioinformatics 07-26-2010, 12:55 AM
Replies: 1
Views: 1,380
Posted By strob
clustering based on SNP information

Dear all,

I have re-sequencing data for many genotypes for the same set of genes. As expected, the differences are minor and are most of the time SNPs. As I want to cluster the genotypes based on...
Forum: Events / Conferences 07-23-2010, 01:26 AM
Replies: 0
Views: 2,731
Posted By strob
The 5th International Conference on Genomics(ICG-V) - China

http://www.genomeconference.org/

The 5th International Conference on Genomics (ICG-V), to be held in Shenzhen, China, November 1518, 2010, will emphasize the latest advances in genomic...
Forum: General 05-31-2010, 10:38 PM
Replies: 26
Views: 10,677
Posted By strob
another player (nanopore sequencing) (Kavli...

another player (nanopore sequencing) (Kavli Institute of Nanoscience, The Netherlands)

Graphene Nanopores Solve DNA Sequencing Problem
http://www.technologyreview.com/blog/arxiv/25252/

The...
Forum: Bioinformatics 05-19-2010, 12:32 AM
Replies: 4
Views: 2,717
Posted By strob
fastx toolkit (incorporated in Galaxy)

fastx toolkit (incorporated in Galaxy)
Forum: De novo discovery 05-12-2010, 12:10 AM
Replies: 4
Views: 4,436
Posted By strob
Why do you need to view your contigs or...

Why do you need to view your contigs or scaffolds? As this is a de novo assembly, the only thing you get back are contigs or scaffolds. You can look at them in a special viewer, but you will see...
Forum: Bioinformatics 04-12-2010, 03:50 AM
Replies: 13
Views: 6,192
Posted By strob
http://www.ebi.ac.uk/~zerbino/oases/ De novo...

http://www.ebi.ac.uk/~zerbino/oases/

De novo transcriptome assembler for very short reads (the RNAseq variant of velvet)
Forum: Bioinformatics 04-11-2010, 11:32 PM
Replies: 10
Views: 3,947
Posted By strob
genome sequencing

genome sequencing
Forum: Bioinformatics 04-08-2010, 12:19 AM
Replies: 15
Views: 5,585
Posted By strob
Just make sure that your training set is quite...

Just make sure that your training set is quite large, preferably experimentally validated genes and as heterogeneous as possible (single exon vs. multi exon genes; long vs. small genes; ...),...
Forum: Bioinformatics 04-08-2010, 12:06 AM
Replies: 15
Views: 5,585
Posted By strob
We use GlimmerHMM, but we use the models which...

We use GlimmerHMM, but we use the models which are provided. We do not have enough validated data to train the models ourselves.
Forum: Bioinformatics 04-07-2010, 10:28 PM
Replies: 10
Views: 3,947
Posted By strob
velvet test

Dear all,

I just received 1 Flow cell of illumina plant sequencing data (75bp PE reads, ~2 X 26 million reads/lane). As we don't have in most cases a reference sequence available, I will have to...
Forum: Bioinformatics 03-31-2010, 06:12 AM
Replies: 17
Views: 26,156
Posted By strob
I receive the same error message when running...

I receive the same error message when running SAMtoBED, downloaded from this site : http://people.virginia.edu/~arq5x/utilities.html

I also created this SAM file from an Bowtie run (-S) (version...
Forum: Bioinformatics 03-23-2010, 07:35 AM
Replies: 12
Views: 2,351
Posted By strob
maybe handy to first read this paper in order to...

maybe handy to first read this paper in order to know what is what:

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

Cock et al, 2009
...
Showing results 1 to 25 of 79

 


All times are GMT -8. The time now is 05:53 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO