User: marit.hetland

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Posts by marit.hetland

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Unable to blast entire coding sequence of gene
... I have the nucleotide sequence of 59 genes from strain NC_000913.3 that I want to blast to extract from 20 other strains. To do this, I am running the below code in a loop in the terminal, where $que is one of the 59 genes and ${i} is one of the 20 strains. blastn -query $que -db ${i} -outfmt ...
genome bacteria alignment blast blastn written 20 months ago by marit.hetland30
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2
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Running assemblies in parallel
... Hello, I have 600+ bacterial isolates (*fastq.gz files) that I want to assemble. I have a script which uses a for loop to trim adapters and run SPAdes on each isolate, but this takes a very long time, and my computer should be powerful enough to run the script for multiple isolates at one time, wh ...
assembly fastq parallel written 20 months ago by marit.hetland30 • updated 20 months ago by Joe14k

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