User: MK2000

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MK200010
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Posts by MK2000

<prev • 9 results • page 1 of 1 • next >
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Downloading BLAST+ executables to remote cluster on Mac
... I am attempting to try and download the BLAST+ executable commands to my terminal on a macOS computer and have access to them on an academic remote computer account. I was able to do it before somehow, but then I deleted it to make room on my disk, and now I can't seem to find anything that works. C ...
software blast download written 4 weeks ago by MK200010
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Comment: C: Genovo Metagenome Assembly
... I downloaded and unpacked Genovo binaries 0.4, which I am running from my mac on a remote computer. I am using ./assemble file.fasta, but receiving the following error: Gibbs Reads... Regular spikes. buildHash done in 0.02 seconds. 1000 2000 3000 assemble: jvAlign.cc:43: jvAlignCache::jvAlignCache( ...
written 5 weeks ago by MK200010
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Genovo Metagenome Assembly
... Can you break up your fasta file containing all metagenomic reads into smaller, separate files and submit these smaller files separately to an assembly program? I am working with 454 data on Genovo assembler and it doesn't seem to want to take files with more than about 300 reads in them. ...
assembly metagenome written 5 weeks ago by MK200010 • updated 5 weeks ago by h.mon23k
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EMBOSS predicting proteins
... I am trying to follow the data analysis of a paper, and they vaguely say "predicted protein sequences from metagenomic reads using EMBOSS". For anyone familiar with EMBOSS features, would you go with getorf command or transeq? Thank you! ...
metagenomics emboss protein prediction written 5 weeks ago by MK200010 • updated 5 weeks ago by h.mon23k
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Filtering and Trimming Metagenomic Data
... I am attempting to run through a whole genome shotgun metagenomics pipeline on some raw metagenomic reads from a hypersaline soil microbial community study on NCBI, and I am stuck on the initial quality control step (I have very little experience in this field). I utilized FastQC and Prinseq to get ...
metagenomics prinseq microbial fastqc written 8 weeks ago by MK200010 • updated 6 weeks ago by Biostar ♦♦ 20
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Forum: Metagenomics Tutoring Opportunity
... Hi all, I was wondering if there was anyone on here that could tutor in metagenomics data processing? I am very new to the field, and I am trying to understand the basics of quality filtering, predicting protein sequences, creating contigs and sequence binning. I am starting from raw reads from a ...
metagenomics tutoring forum microbial written 8 weeks ago by MK200010 • updated 8 weeks ago by h.mon23k
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Genotype Extraction Format from VCF file
... When you extract genotype data for certain samples in a VCF file, is the resultant file in GT.FORMAT still technically a VCF file in itself? or if you wanted these extracted genotypes in their own vcf, do you somehow have to convert this to .vcf? ...
vcf terminal sequencing written 9 weeks ago by MK200010 • updated 9 weeks ago by WouterDeCoster36k
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Comment: C: BEDOPS installation on MAC
... Hello Alex, Thanks for your comment. I am able to run through the installer package from the Releases page with success (or though it seems). However, the vcf2bed command is still not recognized when I go to use it in terminal. I feel the error could be with this step in the installation: "BEDOPS ...
written 10 weeks ago by MK200010
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BEDOPS installation on MAC
... Hello! I am very new to programming and working with omics data in general, but I am trying to convert a VCF file to a BED file in my terminal on MacOS. I was interested in downloading the BEDOPS tool package and using the vcf2bed command. I then downloaded the latest version of BEDOPS, per instruc ...
assembly bedops written 10 weeks ago by MK200010 • updated 10 weeks ago by Alex Reynolds27k

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