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Forum: Academic/Non-Profit Jobs 08-12-2016, 06:36 AM
Replies: 0
Views: 736
Posted By blancha
Bioinformatics analyst at IRCM, Montreal, Canada

Summary of responsibilities
The successful candidate will work in the collection, management, interpretation, and analysis of biological/clinical data, with a focus on deep or next-generation...
Forum: Bioinformatics 06-15-2016, 12:22 PM
Replies: 4
Views: 1,931
Posted By blancha
I process NGS data all day long. I have never...

I process NGS data all day long.
I have never used the GPU cores available on our cluster.
I'd be really curious to know though what the potential benefits of using software capable of running on...
Forum: Bioinformatics 03-24-2016, 08:35 AM
Replies: 2
Views: 1,688
Posted By blancha
No need to reinvent the wheel, and write your own...

No need to reinvent the wheel, and write your own script.

Just download the ClinVar variants in the VCF format, and use SnpSift Annotate to annotate your own VCF file with the downloaded VCF file....
Forum: Vendor Forum 02-25-2016, 06:54 AM
Replies: 7
Views: 2,301
Posted By blancha
Clickbait. Amend the title or delete the post. ...

Clickbait.
Amend the title or delete the post.
The correct title should be:
Genotypic announces $39 whole exomes data analysis
Forum: General 02-23-2016, 06:43 AM
Replies: 10
Views: 13,208
Posted By blancha
EMBOSS is an old program, but it works remarkably...

EMBOSS is an old program, but it works remarkably well for this type of task.
Don't be fooled by the dated website.
It is a very efficient program....
Forum: Bioinformatics 02-20-2016, 09:42 AM
Replies: 3
Views: 2,039
Posted By blancha
Yes, with the caveat that both types of cells...

Yes, with the caveat that both types of cells should produce the same amount of total RNA per cell, which is generally the case.

To understand the concept better, you should really think of read...
Forum: Bioinformatics 02-20-2016, 06:42 AM
Replies: 3
Views: 2,039
Posted By blancha
No, you are comparing apples and oranges. ...

No, you are comparing apples and oranges.

The small RNAs are filtered out during the standard RNA-Seq protocol.
The small RNAs are selected during the small RNA-Seq protocol.
How then can you...
Forum: Bioinformatics 02-19-2016, 02:05 AM
Replies: 4
Views: 1,848
Posted By blancha
We never use the ERCC spike-ins. They are an...

We never use the ERCC spike-ins.
They are an added cost and hassle of dubious benefit.

The main issue, confirmed independently in several studies, is that the reliability of the spike-ins...
Forum: Bioinformatics 02-16-2016, 12:24 PM
Replies: 3
Views: 1,730
Posted By blancha
I had the same problem. Perhaps the users on...

I had the same problem.
Perhaps the users on the Bioconductor support forum have more helpful suggestions.
https://support.bioconductor.org/
Forum: Bioinformatics 02-16-2016, 06:11 AM
Replies: 3
Views: 1,730
Posted By blancha
The only way that I know is slow and painful. ...

The only way that I know is slow and painful.

You first have to install the version of R compatible with the version of Bioconductor, R-2.11 in this case.
I then use install.packages to install...
Forum: Bioinformatics 02-15-2016, 09:37 AM
Replies: 2
Views: 1,244
Posted By blancha
There is no single answer to this question, so...

There is no single answer to this question, so I'll list some of the best-known languages in decreasing order of importance in bioinformatics.

#1 R, if only because of Bioconductor

#2 Python,...
Forum: RNA Sequencing 02-08-2016, 04:35 PM
Replies: 4
Views: 2,500
Posted By blancha
I don't understand your post. You either do...

I don't understand your post.
You either do ribo-depletion or poly-A enrichment, not both.
You have to pick one or the other, or you will be sequencing mainly rRNA, which is not very useful.
Forum: Bioinformatics 02-05-2016, 04:22 PM
Replies: 1
Views: 838
Posted By blancha
http://www.bioconductor.org/help/workflows/rnaseqG...

http://www.bioconductor.org/help/workflows/rnaseqGene/#count
Forum: Bioinformatics 02-05-2016, 03:15 PM
Replies: 2
Views: 915
Posted By blancha
I don't see the utility of this particular...

I don't see the utility of this particular program.
I don't see anything wrong with an individual lab storing their data on a network drive.
If they do want to use software to manage their data, it...
Forum: RNA Sequencing 02-05-2016, 12:31 PM
Replies: 4
Views: 1,301
Posted By blancha
I agree with dpryan. sessionInfo() will give...

I agree with dpryan.
sessionInfo() will give more details about the attached packages.
Check which packages differ from our setup.
Perhaps you just need to update GenomicRanges.
In the worse case...
Forum: RNA Sequencing 02-05-2016, 11:32 AM
Replies: 4
Views: 1,301
Posted By blancha
The first step when a bug is encountered is...

The first step when a bug is encountered is always to update to the latest version of the program available, before reporting the bug.

Check your version of DEXSeq.
If it's not 1.16.8, start by...
Forum: Bioinformatics 01-14-2016, 11:20 AM
Replies: 3
Views: 1,148
Posted By blancha
In Canada, with a Master's and between 2 and 5...

In Canada, with a Master's and between 2 and 5 years experience, a good salary is about 60,000 CAD/year.
As a comparison, many computer science graduates with just a bachelor's degree, will be...
Forum: Bioinformatics 01-14-2016, 10:58 AM
Replies: 3
Views: 1,148
Posted By blancha
You must be out of your mind! I actually did...

You must be out of your mind!

I actually did work with one medical school graduate who did not complete his residency, and switched to a master's in bioinformatics.
He then proceeded to leave his...
Forum: Introductions 01-06-2016, 12:51 PM
Replies: 2
Views: 1,070
Posted By blancha
If you're serious about bioinformatics, you'll...

If you're serious about bioinformatics, you'll have to learn both unfortunately, however confusing that may be.

The one, irreplaceable, feature of R that cannot be found in Python is the library...
Forum: Bioinformatics 01-03-2016, 03:59 PM
Replies: 4
Views: 2,676
Posted By blancha
I have no idea, but I wouldn't start a filename...

I have no idea, but I wouldn't start a filename with an underscore.
Forum: Bioinformatics 12-11-2015, 01:34 PM
Replies: 6
Views: 4,537
Posted By blancha
I find it quicker to just switch to Python, when...

I find it quicker to just switch to Python, when the scripts become too complicated.

I have a Python script that splits the filename, into sample name and lane number. It then groups together the...
Forum: RNA Sequencing 12-11-2015, 01:16 AM
Replies: 4
Views: 1,263
Posted By blancha
Sorry, I don't know the answer. Looks correct...

Sorry, I don't know the answer.
Looks correct to me.
Other than suggesting to update CummeRbund If you have an ancient version, older than 2.7.3, I don't have any solutions to propose to this...
Forum: RNA Sequencing 12-10-2015, 11:19 PM
Replies: 4
Views: 1,263
Posted By blancha
What is the content of...

What is the content of E:/cuff_out/read_groups.info?
What command was used to run Cuffdiff?
Also, perhaps not necessary, were there any error messages during the Cuffdiff run?
Forum: Bioinformatics 12-09-2015, 06:40 PM
Replies: 6
Views: 4,537
Posted By blancha
for i in {13..14}; do for j in 1 2; do cat...

for i in {13..14}; do for j in 1 2; do cat HC${i}_S${i}_*_R${j}_001.fastq > HC${i}_S${i}_R${j}_001.fastq; done; done


I do have a more sophisticated Python script that can handle cases when no...
Forum: Bioinformatics 12-09-2015, 06:46 AM
Replies: 14
Views: 2,589
Posted By blancha
Our local server, at our institute, has 580 GB of...

Our local server, at our institute, has 580 GB of shared memory.
So, RAM is generally not an issue. :)

On the Compute Canada cluster, each core requested comes with 2.7 GB RAM, which is generally...
Showing results 1 to 25 of 367

 


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