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 4 weeks 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 8 weeks ago by
pld ♦ 4.5k
1
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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 9 weeks ago by
pld ♦ 4.5k
0
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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 11 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 11 weeks ago by
pld ♦ 4.5k
1
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... BASH has an until loop: http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_09_03.html ...
written 3 months ago by
pld ♦ 4.5k
0
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1
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205
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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 4 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 4 months ago by
pld ♦ 4.5k
0
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3
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310
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... Have you explored making a custom database for Kraken? ...
written 4 months ago by
pld ♦ 4.5k
0
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2
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511
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... I would personally love to see some better visualizations of transcriptome assembly quality. ...
written 4 months ago by
pld ♦ 4.5k
Latest awards to pld
Scholar
29 days ago,
created an answer that has been accepted.
For A: difference between "predicted coding region" and "Hypothetical Protein
Commentator
4 weeks 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
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.
Popular Question
4 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question
4 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated
4 months ago,
created a post with more than 5 votes.
For C: Studying Bioinformatics - Reasons, motives and career
Appreciated
4 months ago,
created a post with more than 5 votes.
For C: Studying Bioinformatics - Reasons, motives and career
Popular Question
4 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.
Popular Question
7 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Commentator
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
Scholar
7 months ago,
created an answer that has been accepted.
For A: difference between "predicted coding region" and "Hypothetical Protein
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
Commentator
8 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
8 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
Commentator
9 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
9 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Commentator
11 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
12 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
Popular Question
12 months ago,
created a question with more than 1,000 views.
For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated
13 months ago,
created a post with more than 5 votes.
For C: Studying Bioinformatics - Reasons, motives and career
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Paper publication without qPCR validation
Commentator
13 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
Commentator
13 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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