User: bgold04

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bgold040
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Posts by bgold04

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Comment: A: Request Efficient Approach to concatenating and compressing PATRIC .fna files
... Thank you for the opportunity to ask a question! ...
written 9 days ago by bgold040
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Comment: C: Request Efficient Approach to concatenating and compressing PATRIC .fna files
... Pretend you are in a class trying to figure out an unknown most definitively in the least possible time. That's the problem I am working on. ...
written 10 days ago by bgold040
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Comment: A: Request Efficient Approach to concatenating and compressing PATRIC .fna files
... Thank you for the very insightful comment, jrj.healey ...
written 10 days ago by bgold040
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Comment: A: Request Efficient Approach to concatenating and compressing PATRIC .fna files
... Thank you for your kind and insightful questions and suggestions. ...
written 10 days ago by bgold040
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Answer: A: Need help with shell script for ftp get PATRIC bacterial sequences
... content deleted by user ...
written 22 days ago by bgold040
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Comment: A: Need help with shell script for ftp get PATRIC bacterial sequences
... content deleted by user ...
written 22 days ago by bgold040
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Comment: C: sed regex code help wanted
... sorry, all the entries do not have 3 items; that's why I asked the question... Thanks for thinking about this though.... -- Bert ...
written 5 weeks ago by bgold040
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sed regex code help wanted
... In an output file, I want to preserve these lines: Prevotella_sp Leptospira_interrogans Leptospira_interrogans Escherichia_coli yet get rid of the alphanumeric and underscore in front of the genus_species in these lines: ADWS01000032_Escherichia_coli EQ973222_Bacteroid ...
microbiome regular expressions sed written 5 weeks ago by bgold040 • updated 5 weeks ago by RamRS17k
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Comment: C: Download All The Bacterial Genomes From Ncbi
... I had to experiment with rattus8's response above because I am working on a MacBook Pro and the extended set of regular expressions requires download of gnu sed (I used homebrew to brew install gsed) and there are some syntax differences.... (NB- I also installed gnu awk using brew install gawk). He ...
written 7 weeks ago by bgold040
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Answer: A: bcftools filter or bcftools isec to EXCLUDE dbSNP snps
... I did this using Wouter DeCoster's suggestion, something like: vcftools --vcf my.vcf --recode --keep-INFO-all --exclude-positions All_20160408.bed It were not pretty making the bed file, and I worry that, because I am excluding by position rather than genotype [eg. A/T at rsXXXXX], I may exclude ...
written 23 months ago by bgold040

Latest awards to bgold04

Popular Question 23 months ago, created a question with more than 1,000 views. For bcftools filter or bcftools isec to EXCLUDE dbSNP snps
Popular Question 23 months ago, created a question with more than 1,000 views. For Requesting help building a bacterial database file consistent with gibVirus.fa

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