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Forum: Bioinformatics 01-06-2011, 12:21 PM
Replies: 1
Views: 1,951
Posted By ntremblay
Hi, have a look at this tool, it works...

Hi,

have a look at this tool, it works perfectly from samtools pileup and you can choose to annotate variation according to many dataset (snp131, 1000g, etc.). Also, the website is well...
Forum: General 01-04-2011, 09:02 AM
Replies: 1
Views: 2,116
Posted By ntremblay
The UCSC Genes track shows gene predictions based...

The UCSC Genes track shows gene predictions based on data from RefSeq, Genbank, CCDS and UniProt. Following all the steps mention in the link you provided, they annotate all the exons to the...
Forum: General 01-04-2011, 08:50 AM
Replies: 3
Views: 1,215
Posted By ntremblay
What kind of experiement are you doing? de novo...

What kind of experiement are you doing? de novo sequencing, exome capture, etc? you can find these information in a standard protocol ...
Forum: Bioinformatics 12-22-2010, 05:39 AM
Replies: 2
Views: 2,089
Posted By ntremblay
Hi, when your are building the dat file...

Hi,

when your are building the dat file specifying your input FASTQ?

you shouldn't see the c.elegans file in the ace file you're getting!

Do you see all your reads stats in the post...
Forum: Webinar Series 12-21-2010, 07:10 PM
Replies: 9
Views: 47,218
Posted By ntremblay
Hi, I would be interested to make a webinar...

Hi,

I would be interested to make a webinar on sequencing tech overview or library prep ... and some specific bioinformatic pipeline like snp discovery from exome capture,

keep me in the...
Forum: Genomic Resequencing 12-21-2010, 02:59 PM
Replies: 3
Views: 2,464
Posted By ntremblay
Our on target rate is about 75% within 100 bp ...

Our on target rate is about 75% within 100 bp ...
Forum: Genomic Resequencing 12-21-2010, 11:16 AM
Replies: 2
Views: 2,961
Posted By ntremblay
Also, if you're looking at structural variation...

Also, if you're looking at structural variation ... a mate-paired library would be ideal.
Forum: Genomic Resequencing 12-21-2010, 11:12 AM
Replies: 3
Views: 2,464
Posted By ntremblay
We have always used 24 hrs hybridization and...

We have always used 24 hrs hybridization and always obtain great results ... also minimizing the hybridization time reduce the evaporation risk and the total hands-on time required.

The only time...
Forum: Service Providers 12-21-2010, 09:37 AM
Replies: 11
Views: 4,104
Posted By ntremblay
The McGill University and Génome Québec...

The McGill University and Génome Québec Innovation Centre (http://www.gqinnovationcenter.com/index.aspx) is a very good facility with a wide array of supported applications and services. From my...
Forum: Sample Prep / Library Generation 12-10-2010, 07:24 AM
Replies: 3
Views: 5,307
Posted By ntremblay
Agencourt Ampure purification kit - exp date

Hi,

does anybody has experienced with an expired ampure kit?

the product datasheet says that the yield is consistent throughout the 12 months shelf life, but I wonder how much it impacts the...
Forum: Bioinformatics 12-06-2010, 01:03 PM
Replies: 1
Views: 2,432
Posted By ntremblay
I'm not familiar with NCBI, but you can...

I'm not familiar with NCBI,

but you can download pairwise or miltiple alignement from UCSC (ie. http://hgdownload.cse.ucsc.edu/downloads.html#human for human vs other species.)

or

you can...
Forum: General 11-30-2010, 01:05 PM
Replies: 4
Views: 2,826
Posted By ntremblay
Hi, try using this tool:...

Hi,

try using this tool: http://idconverter.bioinfo.cnio.es/IDconverter.php

it's very good to convert various ID's, give you the result on screen or txt/excel file and you can chose wich...
Forum: General 11-30-2010, 12:57 PM
Replies: 2
Views: 2,155
Posted By ntremblay
Hi, You have most of the Illumina primer...

Hi,

You have most of the Illumina primer sequence in the attached pdf file!

cheers,
Forum: Sample Prep / Library Generation 11-30-2010, 05:52 AM
Replies: 3
Views: 5,624
Posted By ntremblay
At the end of the day, both kit are basically the...

At the end of the day, both kit are basically the same ... but the 50Mb kit gives a more comprehensive coverage of the actual exome (100% of CCDS - march 2009) and some miRNA and likes...

As for...
Forum: Sample Prep / Library Generation 11-30-2010, 05:41 AM
Replies: 23
Views: 11,875
Posted By ntremblay
The SureSelect kit is by far the reference right...

The SureSelect kit is by far the reference right now, most of the resequencing project have adopted it. With the new 50 Mb version, this kit has increased it's coverage of all exons annotated in the...
Forum: Bioinformatics 11-29-2010, 11:28 AM
Replies: 9
Views: 9,535
Posted By ntremblay
Hi, I've used this tool to analyse whole exome...

Hi, I've used this tool to analyse whole exome data generated on Illumina GaIIx.

The tool is user friendly, the various parameters are all customizable and the interface, although tedious by time...
Forum: Genomic Resequencing 11-26-2010, 09:08 AM
Replies: 2
Views: 1,808
Posted By ntremblay
Hi, you can use any scripts or tools that...

Hi,

you can use any scripts or tools that intersect parameter such as rsID or chromosomal positions to compare a set of snp called from different sample...

Excel can do the job for exome...
Forum: Genomic Resequencing 11-26-2010, 08:58 AM
Replies: 5
Views: 2,546
Posted By ntremblay
Hi, if you encounter an interesting SNP in...

Hi,

if you encounter an interesting SNP in your analysis, the quickest way to determine if it's real or not would be to confirm it with an independant method like PCR + Sanger ...
Forum: Genomic Resequencing 11-26-2010, 08:52 AM
Replies: 7
Views: 2,795
Posted By ntremblay
You could use a lot of techniques to validate a...

You could use a lot of techniques to validate a snp! The traditional way of doing it is PCR + Sanger seq, but new techniques like Taq Man assay, Sequenom Assay, Allelic discrimination with a melting...
Forum: Bioinformatics 11-25-2010, 12:55 PM
Replies: 7
Views: 2,211
Posted By ntremblay
He'res some information from the sra-dump...

He'res some information from the sra-dump instructions (http://www.ncbi.nlm.nih.gov/books/NBK49294/):

3.3 Example:

toolkit installed in: /gold/sra/bin64/

downloaded SRR (contains directory...
Forum: Bioinformatics 11-25-2010, 12:48 PM
Replies: 16
Views: 4,318
Posted By ntremblay
I would say it is a non-synonymous mutation as it...

I would say it is a non-synonymous mutation as it cause a change in the translated amino acid sequence ...!
Forum: Bioinformatics 11-24-2010, 08:52 AM
Replies: 2
Views: 2,174
Posted By ntremblay
Hi, have you tried from your terminal,...

Hi,

have you tried from your terminal, samtools index xxx.bam? this should work to index your file if you have a compiled samtools executable ...

if i'm not mistaken the bam_index.c and...
Forum: Bioinformatics 07-19-2010, 09:39 AM
Replies: 0
Views: 1,531
Posted By ntremblay
ROAST software for SNP/InDel

Hi,

does anybody knows were to download ROAST? I've tried to google/ncbi this program and I can't seem to find it!

see https://wiki.nbic.nl/index.php/Next_Generation_Sequencing:_SNP_Expertise...
Forum: Bioinformatics 06-29-2010, 01:18 PM
Replies: 29
Views: 27,112
Posted By ntremblay
Hey, Galaxy has a tool called FASTQ Groomer under...

Hey, Galaxy has a tool called FASTQ Groomer under NGS: QC and manipulation menu.
you can convert bw various quality format (sanger, solexa, Illumina 1.3 and above, colorspace sanger).

I think...
Forum: Bioinformatics 05-15-2010, 08:18 AM
Replies: 3
Views: 2,525
Posted By ntremblay
Hi, you can view the user guide at...

Hi,

you can view the user guide at http://samtools.sourceforge.net/samtools.shtml

Basically, Samtools is a utility that enable you to manipulate SAM/BAM alignment files.

What are you...
Showing results 1 to 25 of 27

 


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