User: rabio

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rabio0
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Posts by rabio

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How to get actual location of CNV from CNVKit
... I know that the CNVkit output is in bins, so I can't get the actual location of the CNV besides the bin. I was wondering if there is a way to get the actual genomic coordinates of a CNV using CNVKit for short read data rather than just finding out the general bin location ...
cnvkit cnv wgs written 8 weeks ago by rabio0 • updated 8 weeks ago by MatthewP190
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Comment: C: Cannot run xtract from entrez direct
... Yes, just replacing it with a dummy word. Thank you so much, that fixed the problem! It works now! ...
written 18 months ago by rabio0
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Comment: C: Cannot run xtract from entrez direct
... echo $PATH returns the following: /Users/username/src/edirect:/Users/username/Documents/SeniorPt1/Lab/miniconda3/bin:/Users/username/miniconda3/bin:/Library/Frameworks/Python.framework/Versions/2.7/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/username/edirect:/Users/use ...
written 18 months ago by rabio0 • updated 18 months ago by genomax70k
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Comment: C: Cannot run xtract from entrez direct
... Yes! And in the directory ~/edirect the following files exist: xtract, xtract.Darwin, and xtract.go. And giving all permissions (chmod 777) does not help either. ...
written 19 months ago by rabio0
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Cannot run xtract from entrez direct
... I have been unable to use xtract function from EDirect, as I get the following message simply by typing "xtract" into terminal: Unable to locate xtract executable. Please execute the following: ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.Darwin.gz gunzip -f xtract.Darwin.gz chmod ...
edirect xtract entrez written 19 months ago by rabio0

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