Moderator: pld

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pld4.8k
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Posts by pld

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Comment: C: Memory-driven computing accelerates genomic data processing
... Is this really a new paradigm, or is this a sign that hardware has but we're still writing code like our nodes are from 5+ years ago? Or are some of us just spoiled and want the software to catch up to us? I was always told that "early on" memory was the main reason people built clusters and went ...
written 9 months ago by pld4.8k
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Comment: C: Memory-driven computing accelerates genomic data processing
... It should, but I've noticed much better performance when I manually put things into /dev/shm/. ...
written 9 months ago by pld4.8k
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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 13 months ago by pld4.8k
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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 15 months ago by pld4.8k
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Comment: C: mRNA to protein
... https://github.com/TransDecoder/TransDecoder/wiki ...
written 18 months ago by pld4.8k
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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 18 months ago by pld4.8k
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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 20 months ago by pld4.8k
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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 2.2 years ago by pld4.8k
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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 2.4 years ago by pld4.8k
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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 2.5 years ago by pld4.8k

Latest awards to pld

Popular Question 10 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Popular Question 11 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Popular Question 13 months ago, created a question with more than 1,000 views. For Large VCF QUAL Values
Popular Question 13 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Scholar 13 months ago, created an answer that has been accepted. For A: difference between "predicted coding region" and "Hypothetical Protein
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Paper publication without qPCR validation
Popular Question 14 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Popular Question 14 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 14 months ago, created a question with more than 1,000 views. For High Mapping but No Reads Properly Paired
Popular Question 14 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 15 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 16 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 17 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 17 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 18 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 19 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 19 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 19 months ago, created a question with more than 1,000 views. For Assemble PCR Product Sanger Sequences
Popular Question 19 months ago, created a question with more than 1,000 views. For Generate a VCF File for Different Reference Sequences
Popular Question 19 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 20 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 20 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 20 months ago, created a question with more than 1,000 views. For Cuffmerge: GFF Error: duplicate/invalid 'transcript'
Popular Question 21 months ago, created a question with more than 1,000 views. For R/Bioconductor: Applying Limma Functions To A Matrix.
Appreciated 23 months ago, created a post with more than 5 votes. For C: Studying Bioinformatics - Reasons, motives and career

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