Moderator: pld
pld ♦ 4.7k
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Posts by pld
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... At the very least just leave the file decompressed... ...
written 5 weeks ago by
pld ♦ 4.7k
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Comment:
C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 3 months ago by
pld ♦ 4.7k
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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 4 months ago by
pld ♦ 4.7k
2
votes
1
answer
286
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... Try Kraken, its faster and can generate the kind of output you are asking for. ...
written 6 months ago by
pld ♦ 4.7k
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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 12 months ago by
pld ♦ 4.7k
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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 15 months ago by
pld ♦ 4.7k
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1
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884
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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 16 months ago by
pld ♦ 4.7k
1
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1
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668
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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 16 months ago by
pld ♦ 4.7k
0
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1
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516
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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 16 months ago by
pld ♦ 4.7k
0
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1
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516
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... First hit when you google "mhc-1 binding dataset".
The third hit is even from an AI lab: http://ailab.ist.psu.edu/red/mhci.html ...
written 16 months ago by
pld ♦ 4.7k
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