User: jnowacki

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jnowacki30
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Posts by jnowacki

<prev • 23 results • page 1 of 3 • next >
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Depth of Coverage - Calculated Per Probe / Bed Region
... I'm trying to find out the average depth of coverage per target region in a bed file. I can easily use bedtools -depth to find the depth of coverage at each base, but I'd much rather have it as average coverage per region. The bedtools "-hist" option produces 110 reports on one of my features. ...
bed bam tool depth written 3 months ago by jnowacki30 • updated 3 months ago by Kevin Blighe17k
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Comment: C: Tool For Counting Adapter Dimer: I need metrics NOT trimming
... but does it report dimers? I'm not concerned with adapters. I'm concerned with adapter dimers that have not library sequence. Thank you for the response. ...
written 8 months ago by jnowacki30
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Tool For Counting Adapter Dimer: I need metrics NOT trimming
... Any tools out there that give adapter dimer metrics? I don't care if they trim or don't trim I just need adapter dimer counts to see how messy our wetlab protocol is. ...
adapter dimer adapters trimming dna primer dimer written 8 months ago by jnowacki30 • updated 8 months ago by chen1.5k
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Metagenomic Mappers & Benchmark Datasets?
... I'm looking to map a mixture of bacteria to known references and classify their abundance. What are the top tools for this? Q1) Top tools for meta-genomics mapping Q2) Control data-sets I can use to verify my metagenomic mapping pipeline? I am familiar with assembly data-sets and tools. For inst ...
metagenomics mapping written 9 months ago by jnowacki30 • updated 9 months ago by Samuel Brady230
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Comment: C: MetaSpades can't access memory? Crashes when requesting 45 Gigs on a 128 Gig RH
... I solved this. It's a combination of two things: 1) Redhat Enterprise 6 does not work but Ubuntu 16 LTS server does 2) Ubuntu server works ONLY if there are at least 3 gigabytes of memory for each core. (according to the software developers). I throttled the assembly down to 6 gigabytes per th ...
written 10 months ago by jnowacki30
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MetaSpades can't access memory? Crashes when requesting 45 Gigs on a 128 Gig RHEL6 machine
... Metaspades can't seem to request memory from a 128 GB Redhat 6 machine. Any ideas? Lowering the CPU and memory flag limits doesn't help. This is from the developer themselves: > Here is what happened: SPAdes used approx 15 Gb of RAM and tried to > allocate 45 Gb of RAM more. However, your ...
metagenomics spades jemalloc malloc metaspades.py written 10 months ago by jnowacki30
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Top microbial WGS (metagenomic) analysis options? Side by Side comparisons
... I found this master list: https://www.biostars.org/p/58279/#90495 But has anyone done a side by side comparison of how each performs when assembling & analyzing frankenbugs? ...
metagenomic microbial written 11 months ago by jnowacki30
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Comment: C: automating multiple fastq.gz -> SAM
... How did you make that graph? ...
written 11 months ago by jnowacki30
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Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
... I was hyper-specialized on the hardware end for about 8 years and now I'm getting back into building pipelines. A LOT has changed since I got my masters. What's are your favorite places to keep up to speed with the best tools & techniques for bioinformatics pipelines? Biostars is obviously a ...
workshops tutorial tutorials blogs conferences written 11 months ago by jnowacki30
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Managing Projects & FastQ files (Getting Organized)
... Tools for managing projects & FastQ files? I'm about to be flooded with data and I need a system to organize everything. What tools are out there that will allow you to: 1) Organize fastq files by project 2) Allow you to search for files / projects that were used several years ago 3) Annot ...
lims organization data management sequencing written 11 months ago by jnowacki30 • updated 11 months ago by Pierre Lindenbaum106k

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