Moderator: pld

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pld4.6k
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Posts by pld

<prev • 657 results • page 1 of 66 • next >
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Comment: C: standalone blastp: increasing word size extremely slows down the search
... 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 3 months ago by pld4.6k
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... 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 6 months ago by pld4.6k
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Comment: C: "Optimal" setting of CPU and max_memory in Trinity
... 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 7 months ago by pld4.6k
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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 7 months ago by pld4.6k
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Comment: C: I want DATA SETS for Machine learning
... 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 8 months ago by pld4.6k
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Comment: C: I want DATA SETS for Machine learning
... 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 8 months ago by pld4.6k
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Comment: C: Problem with using "until" in "bash script"
... BASH has an until loop: http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_09_03.html ...
written 8 months ago by pld4.6k
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Comment: C: RNA Seq analysis of virally infected cells
... 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 9 months ago by pld4.6k
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Comment: C: More than 300.000 peaks for a viral transcription factor - what could this mean?
... 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 10 months ago by pld4.6k
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Comment: C: Softwares for Bacterial/Viral Classification from RNAseq
... Have you explored making a custom database for Kraken? ...
written 10 months ago by pld4.6k

Latest awards to pld

Appreciated 26 days ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Popular Question 5 weeks ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 8 weeks ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 11 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 Cuffmerge: GFF Error: duplicate/invalid 'transcript'
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 5 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Commentator 5 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 5 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 5 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Scholar 6 months ago, created an answer that has been accepted. For A: difference between "predicted coding region" and "Hypothetical Protein
Commentator 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
Popular Question 7 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 8 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 9 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 9 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Popular Question 9 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 10 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
Popular Question 10 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 11 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Popular Question 12 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
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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