Moderator: pld
pld ♦ 4.5k
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Posts by pld
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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 1 day ago by
pld ♦ 4.5k
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 29 days ago by
pld ♦ 4.5k
1
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151
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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 5 weeks ago by
pld ♦ 4.5k
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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 7 weeks ago by
pld ♦ 4.5k
0
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1
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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 7 weeks ago by
pld ♦ 4.5k
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... BASH has an until loop: http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_09_03.html ...
written 8 weeks ago by
pld ♦ 4.5k
0
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1
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... If you're working with a RNA virus, remember you'll have to find a way to differentiate between genome (and any genomic intermediates) and viral mRNA. ...
written 3 months ago by
pld ♦ 4.5k
0
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6
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1.2k
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6
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... You said "expressed the TF", this would be in transfected cells, or were they infected with virus? Do you have a control in your RNA-Seq experiments (e.g. transfected for a non-TF EBV protein)? It would be important to know if the DEGs you've found are in response to the TF specifically and not in r ...
written 3 months ago by
pld ♦ 4.5k
0
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3
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279
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... Have you explored making a custom database for Kraken? ...
written 3 months ago by
pld ♦ 4.5k
0
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2
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478
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... I would personally love to see some better visualizations of transcriptome assembly quality. ...
written 3 months ago by
pld ♦ 4.5k
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4 weeks ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question
3 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: Studying Bioinformatics - Reasons, motives and career
Popular Question
3 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated
3 months ago,
created a post with more than 5 votes.
For C: Studying Bioinformatics - Reasons, motives and career
Popular Question
3 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question
5 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question
6 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
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6 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar
6 months ago,
created an answer that has been accepted.
For A: difference between "predicted coding region" and "Hypothetical Protein
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
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7 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
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7 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Popular Question
8 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Commentator
10 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
Popular Question
11 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated
12 months ago,
created a post with more than 5 votes.
For C: Studying Bioinformatics - Reasons, motives and career
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
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12 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
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12 months ago,
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For A: I want to re-open the old debate: python or perl ?
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12 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
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