User: owenz

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owenz10
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1 year, 1 month ago
Joined:
1 year, 6 months ago
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o*********@gmail.com

Posts by owenz

<prev • 21 results • page 1 of 3 • next >
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Comment: A: Jellyfish version problem Kraken
... The problem now seems to be to limit hash size on a 32gb Ram PC. What should be ideal? ...
written 13 months ago by owenz10
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Jellyfish version problem Kraken
... I installed Kraken on Linux and was about to build the bacterial db. Unfortunately, the Jellyfish version installed was 2.2.8 which is not compatible with Kraken. I uninstalled this version and tried to install the necessary 1.1.11 version through apt. Unfortunately it was not retrieved. I downloa ...
kraken jellyfish written 13 months ago by owenz10
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Comment: C: How do you align to multiple reference genomes?
... I see. Sounds complicated for me to implement. No there is no target capture involved. Thanks for your help ...
written 18 months ago by owenz10
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Comment: C: How do you align to multiple reference genomes?
... No worries. I am fairly green myself. The NS5B gene is most often used for genotyping HepC. Different SNPs in the gene will affect the particular genotype [as far as I know] ...
written 18 months ago by owenz10
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Comment: C: How do you align to multiple reference genomes?
... I heard about GNU parallel but haven't really tested it out. Thanks for the suggestion ...
written 18 months ago by owenz10
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Comment: C: How do you align to multiple reference genomes?
... Most samples tend to have one major genotype but it is not uncommon to have 2 genotypes. In the case of a unique genotype, how do I align independently? I was trying to implement running multiple scripts (one for each reference) placed in a master script but I was getting a bunch of errors. I tried ...
written 18 months ago by owenz10
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How do you align to multiple reference genomes?
... I am in the process of finishing a small script which I will use to determine the genotype of Hepatitis C FASTQ samples. Hepatitis C has 7 known genotypes. I would like to be able to feed FASTQ files to the script and they are aligned to all the 7 genotypes, and then obtain the most likely genotype ...
hepatitis next-gen alignment sequencing written 18 months ago by owenz10
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Comment: C: Nested for loop in Bash
... Yes that is the post that solved it. Thanks ...
written 18 months ago by owenz10
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Comment: A: Nested for loop in Bash
... Thanks a lot for your help ...
written 18 months ago by owenz10
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Comment: C: Nested for loop in Bash
... I see. Can you explain what do the xargs flags do in this case? ...
written 18 months ago by owenz10

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