Former User of DNAx Community_28
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Recent activity by Former User of DNAx Community_28
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It is not only possible, it is quite easy. 1) Write your script.2a) make a directory in your project called scripts and (b) upload your new script there.3) In the dx command proper, execute the scr...
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Iris, Double check the gene set that you want. Your command as written is looking for a nonexistent gene set: "--extract-setlist "GeneX(ENSG00000XXXX)" \ " You need to pick a gene that exists in th...
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For an earlier release of the GWS data, I wrote a qucik dx script to list all the vcf files for a given chromosome, sort them on ascending order and then write aout a file for the samtools merge co...
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The scripts (partB-G) assume that you are running them from a LOCAL command line and not from within a jupyter notebook. Once the phenotype/covariate file is created and saved back to the project, ...
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For those who cannot attend, will the workshop be recorded and available offline?
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I am not sure why you are having this issue. Forgive me for being slow, but it has been over a year since I wrote this repo, but the scripts I wrote have a specific order for analysis. Lets go over...
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The output of 16a is the association text file for chromosomes 1-22+X that you can use in locuszoom.?
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The next script 15a runs a gwas on each chromosome. ?16a combines all the results together.
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You need to generate a phenotype file, upload it to your project, and replace the name in the script with? the name you gave your phenotype file. The same will be true for the covariate file.?
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I just updated the README files for clearer explanation. see both the base readme as well as the gwas readme.https://github.com/pjgreer/ukb-rap-toolsandhttps://github.com/pjgreer/ukb-rap-tools/tree...
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