User: jnowacki

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jnowacki60
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Posts by jnowacki

<prev • 24 results • page 1 of 3 • next >
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(Closed) Punching a hole in firewall -- to install cutadapt via pip (What ports, ip, protocol, address?)
... I'm trying to request our very security conscious IT team to open up ports so I can get to cutadapt. I need to know port, protocol & IP address. Any help? I found this link https://stackoverflow.com/questions/22377175/what-ports-does-pip-use which says Port - 3128 Port - 443 (confl ...
firewall security pip written 5 months ago by jnowacki60
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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 9 months ago by jnowacki60 • updated 9 months ago by Kevin Blighe30k
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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 14 months ago by jnowacki60
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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 14 months ago by jnowacki60 • updated 14 months ago by chen1.7k
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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 15 months ago by jnowacki60 • updated 15 months ago by Samuel Brady240
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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 15 months ago by jnowacki60
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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 16 months ago by jnowacki60
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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 17 months ago by jnowacki60
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Comment: C: automating multiple fastq.gz -> SAM
... How did you make that graph? ...
written 17 months ago by jnowacki60
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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 17 months ago by jnowacki60

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