Forum: Academic/Non-Profit Jobs
08-12-2016, 07:36 AM
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Replies: 0
Views: 1,009
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...
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Forum: Bioinformatics
06-15-2016, 01:22 PM
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Replies: 4
Views: 2,338
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...
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Forum: Bioinformatics
03-24-2016, 09:35 AM
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Replies: 2
Views: 2,357
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Forum: Vendor Forum
02-25-2016, 07:54 AM
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Replies: 7
Views: 2,691
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Forum: General
02-23-2016, 07:43 AM
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Replies: 10
Views: 14,194
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Forum: Bioinformatics
02-20-2016, 10:42 AM
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Replies: 3
Views: 2,682
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...
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Forum: Bioinformatics
02-20-2016, 07:42 AM
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Replies: 3
Views: 2,682
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...
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Forum: Bioinformatics
02-19-2016, 03:05 AM
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Replies: 4
Views: 2,375
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...
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Forum: Bioinformatics
02-16-2016, 01:24 PM
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Replies: 3
Views: 2,086
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Forum: Bioinformatics
02-16-2016, 07:11 AM
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Replies: 3
Views: 2,086
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...
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Forum: Bioinformatics
02-15-2016, 10:37 AM
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Replies: 2
Views: 1,893
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Forum: RNA Sequencing
02-08-2016, 05:35 PM
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Replies: 4
Views: 2,878
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.
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Forum: Bioinformatics
02-05-2016, 05:22 PM
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Replies: 1
Views: 1,259
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Forum: Bioinformatics
02-05-2016, 04:15 PM
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Replies: 2
Views: 1,158
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...
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Forum: RNA Sequencing
02-05-2016, 01:31 PM
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Replies: 4
Views: 1,551
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...
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Forum: RNA Sequencing
02-05-2016, 12:32 PM
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Replies: 4
Views: 1,551
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...
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Forum: Bioinformatics
01-14-2016, 12:20 PM
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Replies: 3
Views: 1,413
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...
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Forum: Bioinformatics
01-14-2016, 11:58 AM
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Replies: 3
Views: 1,413
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...
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Forum: Introductions
01-06-2016, 01:51 PM
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Replies: 2
Views: 1,242
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...
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Forum: Bioinformatics
01-03-2016, 04:59 PM
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Replies: 4
Views: 3,106
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Forum: Bioinformatics
12-11-2015, 02:34 PM
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Replies: 6
Views: 5,972
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Forum: RNA Sequencing
12-11-2015, 02:16 AM
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Replies: 4
Views: 1,446
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...
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Forum: RNA Sequencing
12-11-2015, 12:19 AM
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Replies: 4
Views: 1,446
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?
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Forum: Bioinformatics
12-09-2015, 07:40 PM
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Replies: 6
Views: 5,972
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...
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Forum: Bioinformatics
12-09-2015, 07:46 AM
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Replies: 14
Views: 3,108
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