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Recent Replies
Answer: Difference between Joint Dimensionality Reduction and Dimensionality Reduction
by
Jean-Karim Heriche
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Dimensionality reduction refers to various methods for transforming a high-dimensional space (i.e. with a lot of variables/features) into a…
Answer: Meta-analysis using 16S rRNA NGS data
by
Antonio R. Franco
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5.0k
Use a regular filter such as Cutadapt, Trimmomatic, Trim-Galore or the like to this end
Comment: scatter plot for DAPC
by
Elisa
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Thank you very much Jean-Karim, the problem is that the points have not the same coordinates, neither the labels cover them: I know this be…
Comment: Different results in finding human sequences from metagenomes (bowtie2 and Krake
by
Antonio R. Franco
★
5.0k
If I don't recall badly, bowtie2 relies in a true alignment, whereas Kraken uses pseudoalignment.
This, in addition to the many options you…
Comment: create 'negative' bed annotation from bed
by
Ram
37k
A small educational note: if an answer was helpful, you should upvote it; **if the answer resolved your question, you should mark it as acc…
Comment: CNVKit does not output all the accessible regions in the targets bed file
by
ashenflower
▴
20
Thank you so much for your reply! I got misleaded by the fact that the NT chromosomes were in the output, so I didn't think the names could…
Comment: How to rename sequence headers
by
Ram
37k
I've restored your post from spam - I don't know why it was flagged in the first place, but from the severe lack of context, I can understa…
Comment: Problems with perl-xml-parser-2.44-4
by
Mensur Dlakic
★
21k
A general way of installing perl modules via CPAN is described [**here**][1]. You will have to find your exact package, but I suspect it mi…
Comment: Advice on aligning error prone NGS reads to a limited number of templates
by
GenoMax
123k
> am interested in a 26bp region near the end of R2.
Then cut these bases out before you align. You can do that with `bbduk.sh` like this:…
Comment: scatter plot for DAPC
by
Jean-Karim Heriche
26k
If your data points pile up on top of each other, this means they have the same coordinates. The solution is to make the coordinates differ…
Comment: How to decide when to have local hardware vs cloud computing?
by
Lluís R.
★
1.1k
There is no pre-existing computation resource yet (neither at the group or the institution level). I will ask the IT team and other bioinfo…
Comment: How to decide when to have local hardware vs cloud computing?
by
Lluís R.
★
1.1k
I was already in a clinical setting (but the resources were only for research like in my current position) and was approved by the IT manag…
Comment: How can I trim this data using Trimmomatic?
by
GenoMax
123k
You may already be planning to but use proper software like Qiime2 to do this analysis: http://qiime.org/tutorials/
Comment: How to decide when to have local hardware vs cloud computing?
by
Dunois
★
2.2k
The question of how to balance the budget allocation between the two would primarily depend upon how much money you have available and how …
Comment: How to decide when to have local hardware vs cloud computing?
by
GenoMax
123k
> Yes, In my previous job I managed a server for 2 years without much
> problems or support, but it is not trivial.
It is good thing that …
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