Comment on "Run miniasm assembler on nanopore reads !"
...sequencing files, you have to concatenate them into a single file prior to runni...n from the example provided in the miniasm documentation; there are other options...ault settings maps the FASTQ reads back to the contigs (the PAF file) created in...2214 days ago
Comment on "poRe: an R package for the visualization and analysis of nanopore sequencing data"
...w.bioconductor.org/biocLite.R") biocLite("rhdf5") install.packages(c("shiny","bit64","data.table","svDialogs")) q() R may ask if you want to install into a local library, just say Y...2221 days ago
Comment on "SPAdes hybrid genome assembly"
...R2627175_2.fastq.gz --nanopore minion.pass.2D.fastq -o SPAdes_hybrid & Use samtools to extract the top contig: head -n 1 SPAdes_hybrid/contigs.fasta samtools faidx SPAd...2221 days ago
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Comment on "Run miniasm assembler on nanopore reads !"
I followed this to assemble the genome using ONT (nanopore reads) Minimap and mi...ep, and therefore the resulting assemblies are contiguous (i.e. long) but very no...a Convert GFA to FASTA: awk '/^S/{print ">"$2"\n"$3}' reads.gfa |...2222 days ago
Comment on "Perl one-liner for bioinformatician !!!"
...ile to lowercase dd $ dd if=input.txt of=output.txt conv=lcase tr $ tr '[:upper:]' '[:lower:]' < input.txt > output.txt awk $ awk '{ print tolower($0) }' input.txt >...2261 days ago
Comment on "How to install Perl modules manually, using CPAN command, and other quick ways"
Install cpanm to make installing other modules easier (you'll thank us later). You need to type these commands into a Terminal emulator (Mac OS X, Win32, Linux) cpan App::cpanminus Now install any module you can find. cpanm Module::Name2265 days ago
Comment on "List of Bioinformatics Vacancy, Jobs, Opportunity websites"
This website is also useful for bioinformatics job hunt https://functionaljobs.com/jobs/2276 days ago
Comment on "Basic command-line to run BLAST"
...s.fr (www.genoscope.cns.fr)|195.83.221.23|:80... connected.HTTP request sent, awaiting response... 200 OKL...n] makeblastdb -in mouse.protein.fa -dbtype prot Building a new DB, current time: 03/14/2018 11:52:20New...2291 days ago
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