Former User of DNAx Community_28
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Recent activity by Former User of DNAx Community_28
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If you are using dx tools on a linux or mac via the command line, you can create a files_to_merge.txt file by running these commands on your local computer: dx ls Bulk/Whole\ genome\ sequences/Who...
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@Vignesh Arunachalam? , First I wrote and published a script to create the list of all the WGS pVCF segments per chromosome here: https://github.com/pjgreer/ukb-rap-tools/blob/main/ukb-vcf-list.sh ...
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I am not sure what type of regeneie analysis you are running, but I wrote a GWAS tutorial a few months ago and the last step of the tutorial is to combine all the association files from each chromo...
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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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