Moderator: pld
pld ♦ 4.8k
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Posts by pld
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... Is this really a new paradigm, or is this a sign that hardware has but we're still writing code like our nodes are from 5+ years ago? Or are some of us just spoiled and want the software to catch up to us?
I was always told that "early on" memory was the main reason people built clusters and went ...
written 9 months ago by
pld ♦ 4.8k
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... It should, but I've noticed much better performance when I manually put things into /dev/shm/. ...
written 9 months ago by
pld ♦ 4.8k
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... 1. Nope, you just guess, then optimize.
2. Nope, not usually. I have a few very lazy scripts that use a ton of RAM (I have it, why not?) they're fast, some things use very little ram and can take a relatively long time.
So, if your goal was to come up with some metric to allocate your job wall time ...
written 13 months ago by
pld ♦ 4.8k
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... At the very least just leave the file decompressed... ...
written 15 months ago by
pld ♦ 4.8k
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Comment:
C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 18 months ago by
pld ♦ 4.8k
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... One thing to consider is that wet lab scientists come to these tools to find sequences for their uses. It's already hard enough to reconcile the gene name reported in a paper (e.g. Hsc70) with the myriad of things with that name (e.g. the 20 or so HSPA8s) before you get to the transcripts.
For a w ...
written 18 months ago by
pld ♦ 4.8k
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... Try Kraken, its faster and can generate the kind of output you are asking for. ...
written 20 months ago by
pld ♦ 4.8k
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... You may be able to save some overhead if you run BLAST directly from the command line, although not likely a meaningful amount. You may also try splitting the database up into multiple parts, just make sure you manually set the statistical options (e.g. dbsize). You'll have to do some post blast wor ...
written 2.2 years ago by
pld ♦ 4.8k
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... I think the paper says that 47% of elements impact the nearest TSS. The 7% is when considering looping interactions only.
> Next we explored whether the relative order of elements in the genome
> affects which long-range interactions occur. It is often assumed that
> distal elements such ...
written 2.4 years ago by
pld ♦ 4.8k
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... It is going to take a while, give it everything you've got. I wouldn't overthink this, you have a single small machine. I'd be more concerned about not having enough ram. ...
written 2.5 years ago by
pld ♦ 4.8k
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For A: difference between "predicted coding region" and "Hypothetical Protein
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For A: Paper publication without qPCR validation
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14 months ago,
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For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
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20 months ago,
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For R/Bioconductor: Applying Limma Functions To A Matrix.
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23 months ago,
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For C: Studying Bioinformatics - Reasons, motives and career
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