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Moderator: pld

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pld ♦ 4.7k
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Posts by pld

<prev • 662 results • page 1 of 67 • next >
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Answer: A: Any suggestions for basic intro to submitting jobs to an HPC cluster?
... 1. Nope, you just guess, then optimize. 2. Nope, not usually. I have a few very lazy scripts that use a ton of RAM (I have it, why not?) they're fast, some things use very little ram and can take a relatively long time. So, if your goal was to come up with some metric to allocate your job wall time ...
written 3 months ago by pld ♦ 4.7k
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Comment: C: How to make bash script operate fast for a 13gb VCF.gz file with 900000 rows and
... At the very least just leave the file decompressed... ...
written 5 months ago by pld ♦ 4.7k
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Comment: C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 7 months ago by pld ♦ 4.7k
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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 7 months ago by pld ♦ 4.7k
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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 10 months ago by pld ♦ 4.7k
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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 15 months ago by pld ♦ 4.7k
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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 18 months ago by pld ♦ 4.7k
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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 19 months ago by pld ♦ 4.7k
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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 20 months ago by pld ♦ 4.7k
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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 20 months ago by pld ♦ 4.7k

Latest awards to pld

Popular Question 22 days ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Popular Question 3 months ago, created a question with more than 1,000 views. For Large VCF QUAL Values
Popular Question 3 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Scholar 3 months ago, created an answer that has been accepted. For A: difference between "predicted coding region" and "Hypothetical Protein
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Popular Question 3 months 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 High Mapping but No Reads Properly Paired
Popular Question 4 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
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 6 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 6 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 6 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 7 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 8 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 8 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 8 months ago, created a question with more than 1,000 views. For Assemble PCR Product Sanger Sequences
Popular Question 8 months ago, created a question with more than 1,000 views. For Generate a VCF File for Different Reference Sequences
Popular Question 9 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 9 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 10 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 10 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 10 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
Popular Question 13 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
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