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Forum: Metagenomics 10-16-2018, 06:55 AM
Replies: 5
Views: 4,277
Posted By ntremblay
Viral RNA was extracted from plasma samples using...

Viral RNA was extracted from plasma samples using QIAamp Viral RNA Mini Kit (720uL of sample) using standard protocol.

Double stranded cDNA synthesis was done using Maxima H Minus Double-Stranded...
Forum: Metagenomics 10-15-2018, 09:17 AM
Replies: 5
Views: 4,277
Posted By ntremblay
@m02846:68:000000000-c39d4:1:1101:14422:2079...

@m02846:68:000000000-c39d4:1:1101:14422:2079 1:n:0:1
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+...
Forum: Metagenomics 10-09-2018, 01:05 PM
Replies: 5
Views: 4,277
Posted By ntremblay
Question AAAAAA.. TTTTTTT.. heterodimers

Good evening all,

I have prepared (ds)cDNA from viral RNA extracted from plasma that was subsequently sequenced on a MiSEQ following standard library preparation.

When I got the reads back, I...
Forum: Bioinformatics 01-06-2011, 12:21 PM
Replies: 1
Views: 2,218
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: 2,579
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: 1,527
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: 2,331
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: 49,692
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: 2,973
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: 3,395
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: 2,973
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: 4,814
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: 6,820
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: 2,741
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: 3,482
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: 2,697
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: 6,210
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: 13,536
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: 10,789
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: 2,292
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: 3,043
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: 3,353
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: 2,511
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: 5,137
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: 2,433
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...
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