Moderator: pld

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pld4.7k
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Posts by pld

<prev • 660 results • page 1 of 66 • next >
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Comment: C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 8 weeks ago by pld4.7k
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Comment: C: Survey: help define Gencode and NCBI primary transcripts
... 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 9 weeks ago by pld4.7k
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Comment: C: Simplest output format of blast contamination check
... Try Kraken, its faster and can generate the kind of output you are asking for. ...
written 4 months ago by pld4.7k
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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 10 months ago by pld4.7k
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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 13 months ago by pld4.7k
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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 14 months ago by pld4.7k
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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 14 months ago by pld4.7k
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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 14 months ago by pld4.7k
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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 14 months ago by pld4.7k
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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 15 months ago by pld4.7k

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Popular Question 17 days ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
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Popular Question 12 weeks ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 3 months ago, created a question with more than 1,000 views. For Assemble PCR Product Sanger Sequences
Popular Question 3 months ago, created a question with more than 1,000 views. For Generate a VCF File for Different Reference Sequences
Popular Question 3 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
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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 Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 4 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.
Appreciated 7 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
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Popular Question 11 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 11 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
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