User: ctseto

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ctseto20
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5 years, 4 months ago
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Posts by ctseto

<prev • 6 results • page 1 of 1 • next >
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Comment: C: WEKA and DNA analysis
... Unless there's a different weka (https://www.cs.waikato.ac.nz/ml/weka/), it's a program used for data mining, written in Java. I don't recall Weka having specific use cases for NGS though, and I'm unsure what "perfectly" means in this context. ...
written 3 days ago by ctseto20
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Answer: A: Filter human parasites from taxonomic profiling with Kraken
... Using CAT (which in turn uses diamond), and then parsing its contig2classification output files by taxonomy may be helpful; everything with a taxonomy tree that descends towards parasites could then be eliminated. ...
written 4 days ago by ctseto20
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Comment: C: col as names
... What does eliminating nrows=3 from read.table() do? Wonder if there's a conflict between header=TRUE and nrows=3... read.table("blah.csv",header=TRUE) should be sufficient. ...
written 6 days ago by ctseto20
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Comment: A: How to recreate FASTQ from BAM
... It's been an eternity, but isn't it -f 64 for R1 and -f 128 for R2 ; per the sam specifications? ...
written 3 months ago by ctseto20
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Comment: C: Strategies To Blast Against Fastq Files
... There's nothing stopping you from stripping the quality lines from a fastq and turning it into a fasta, then running the sequences in blast. Not sure what'd you get out of it asides from a nearest match for each read to a member of your index. Are you trying to count something, map something or assi ...
written 2.3 years ago by ctseto20
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Answer: A: Download All The Bacterial Genomes From Ncbi
... Slight change to the syntax required for those pulling from bacteria. From example output, the directory structure : ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000149845.2_SJ5/GCF_000149845.2_SJ5_genomic.fna.gz An example of column 20 from the bacteria assembly summary: ftp://ftp.ncbi.nl ...
written 2.4 years ago by ctseto20

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