User: steve

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Posts by steve

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Comment: C: Which database software is better for bioinformatics web development? MySQL or M
... in light of the 'bioinformatics' side of the question, I think it also becomes important to consider *where* you plan to run the app from. A lot of bioinformatics work takes place on shared systems like HPC's, which have restricted user-rights and software access; in these cases, I end up going with ...
written 1 day ago by steve1.7k
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Comment: C: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
... Can you describe how the function of this is different from the standard [`bcl2fastq`](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)? From the looks of your script, you are starting with .fastq files (`bcl2fastq` starts from .bcl), not sure how much ...
written 1 day ago by steve1.7k
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Comment: C: Constructing a database for NGS data
... What you are describing is called a LIMS or LIS. There are a million already available, you're better off trying them first instead of reinventing the wheel ...
written 4 days ago by steve1.7k
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Calculating breadth of coverage for TCGA Whole Exome Sequencing data
... I downloaded a set of .maf files from TCGA, which appear to come from whole exome sequencing datasets (labeled as "WXS"). I need to know the breadth of coverage, i.e. number of megabases, for each data set. Where do you get this value from? Is there a definitive resource that lists the number of ...
tcga coverage written 5 days ago by steve1.7k
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Comment: C: Download all DNA mutations from TCGA
... Looks like this URL is no longer working ...
written 9 days ago by steve1.7k
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Comment: C: How to submit multithreaded jobs on SLURM and determine number of threads?
... The issue this targets is the situation where a node has e.g. 7 slots available and you requested 8, I'd rather just take the 7 than wait for a full 8 to open up. Similarly when you have a CPU slot quota that does not divide evenly across your resource allocation, let the last jobs in your queue sq ...
written 11 days ago by steve1.7k
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Comment: C: How to submit multithreaded jobs on SLURM and determine number of threads?
... I see. Typically, the point is not to specify in the script how many threads, but instead get the number of threads from the amount allocated by the scheduler. ...
written 11 days ago by steve1.7k
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Comment: C: How to submit multithreaded jobs on SLURM and determine number of threads?
... Thanks I'm using this with Nextflow so I'll need the `sbatch` format. However this doesn't show how to use a range of threads, or how your script can know how many threads it was given ...
written 11 days ago by steve1.7k
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How to submit multithreaded jobs on SLURM and determine number of threads?
... Really simple question but for some reason I cannot find a simple answer to this. We are moving from SGE to SLURM on our HPC. On SGE, we often submit a job with a range of threads, then inside the job, read the number of threads we got and use that to configure multithreaded programs. Example: ...
slurm written 11 days ago by steve1.7k • updated 11 days ago by Devon Ryan84k
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Comment: C: How do I perform a motif search on a specific fasta sequence?
... If you already have the fasta file then I would just use MEME-ChIP; http://meme-suite.org/tools/meme-chip ...
written 12 days ago by steve1.7k

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