User: cookersjs

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cookersjs10
Reputation:
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Status:
New User
Location:
Toronto, ON
Last seen:
10 hours ago
Joined:
10 months, 3 weeks ago
Email:
c********@gmail.com

Posts by cookersjs

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Last column in UCSC cytoBands.txt files
... Thanks! Seems intuitive enough now, the 'g' threw me off. ...
written 16 hours ago by cookersjs10
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Last column in UCSC cytoBands.txt files
... The file for chromosomal banding coordinates provided by UCSC (cytoBands.txt) has 5 columns like so: chr1 0 2300000 p36.33 gneg chr1 2300000 5300000 p36.32 gpos25 chr1 5300000 7100000 p36.31 gneg chr1 7100000 9200000 p36.23 gpos25 chr1 9200000 12600000 p36.22 gneg I am not sur ...
karyotype ucsc written 17 hours ago by cookersjs10
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Comment: C: Database for Somatic Copy Numbers
... Thanks very much, I believe that COSMICs copy number data actually comes from both TCGA and ICGC, but I hadn't thought to try cbioportal -- definitely will! ...
written 12 days ago by cookersjs10
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Database for Somatic Copy Numbers
... Hello! I am interested in, as the title implies, a relatively up-to-date database that contains information on copy number variation. I know COSMIC offers it, but I am not sure that they are somatic. I am inclined to think that they are, given they are the Catalogue of **Somatic** Mutations in Canc ...
database copy number variation written 13 days ago by cookersjs10 • updated 12 days ago by Max Ivon110
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Comment: C: Extracting VCF information to use in LiftOver
... Thanks very much, I'll make sure to do that! ...
written 9 weeks ago by cookersjs10
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Extracting VCF information to use in LiftOver
... Good day, I am interested in using UCSC's LiftOver tool to convert from GRCh37 to 38. Since VCF's only have the single position in the file, is there any reason I couldn't use the position as both the start and end values? The reason i'm interested in LiftOver particularly, is that they have the f ...
vcf liftover written 9 weeks ago by cookersjs10 • updated 9 weeks ago by Pierre Lindenbaum98k
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How to connect to COSMIC sftp server using Net::SFTP in Perl
... Hello, I am attempting to write code in perl that would allow me to download files from COSMICs SFTP server. I have never done this and I believe that is the major source of my troubles. I have been able to login using HTTP::Request::Common at [https://cancer.sanger.ac.uk/cosmic/login][1], but in t ...
perl cosmic sftp ubuntu written 10 months ago by cookersjs10 • updated 9 months ago by Biostar ♦♦ 20
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Answer: A: Issues with variant effect predictor installation
... So the solution I found to this problem was to find the option near the beginning of the install file "our $use_curl = 0;" around line 54 and change it to "our $use_curl =1;". This allowed the Installer to download the problem files using a different method, rather then the LWP::Simple that is use ...
written 10 months ago by cookersjs10
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Issues with variant effect predictor installation
... I am trying to install Ensembl's variant effect predictor and have run into an installation issue right off the bat. I downloaded the VEP zip file from , unpackaged it and then ran `perl INSTALL.pl`inside ~/ensembl-tools-release-86/scripts/variant_effect_predictor When I run it, this is the output ...
perl ubuntu vep variant effect predictor written 10 months ago by cookersjs10

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