Moderator: pld
pld ♦ 4.7k
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Posts by pld
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3
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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 7 weeks ago by
pld ♦ 4.7k
1
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874
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... At the very least just leave the file decompressed... ...
written 3 months ago by
pld ♦ 4.7k
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3
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253
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3
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Comment:
C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 5 months ago by
pld ♦ 4.7k
0
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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 6 months ago by
pld ♦ 4.7k
2
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1
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348
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... Try Kraken, its faster and can generate the kind of output you are asking for. ...
written 8 months ago by
pld ♦ 4.7k
0
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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 14 months ago by
pld ♦ 4.7k
3
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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 17 months ago by
pld ♦ 4.7k
0
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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 18 months ago by
pld ♦ 4.7k
1
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1
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811
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1
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Comment:
C: STAR command gets Killed
... HPC clusters all tend to have their own rules, features and etc. I have a feeling this might be a problem with how you're trying to run the job and not with STAR. Your cluster should have some kind of support team that should be better equipped to handle this issue.
Assuming you're running Slurm, t ...
written 18 months ago by
pld ♦ 4.7k
0
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1
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553
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... It even shows up on bing (near the bottom)!
https://www.bing.com/search?q=mhc-1+binding+dataset&qs=n&form=QBLH&sp=-1&pq=mhc-1+binding+data&sc=0-18&sk=&cvid=D10100E784BF49CA8910BDB23DE298A4 ...
written 18 months ago by
pld ♦ 4.7k
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