User: offspring18213

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Posts by offspring18213

<prev • 6 results • page 1 of 1 • next >
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Comment: C: data concatenated into Pseudochromosome_1 and 2 for some reason
... Hi, thanks for the response. I use the command "plink --vcf filename --allow-extra-chr --recode --out filename" to convert my vcf to a ped for analysis. Then, when I run the analysis, I am told "number of chromosomes detected: 2". If I do not enter the code "--allow-extra-chr" in plink, then my ana ...
written 19 days ago by offspring182130
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data concatenated into Pseudochromosome_1 and 2 for some reason
... Hi all, I am converting my vcf file to various formats, and have noticed a problem: my dataset is only showing "Pseudochromosome_1" and "Pseudochromosome_2"...when I have 33 chromosomes in my dataset. Also, when I run my analyses, programs (i.e., SNeP, plink) read my data as residing on these two ...
genome written 20 days ago by offspring182130
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Comment: C: pseudochromosomes in VCFtools
... Thank you! This helped a lot. Now, my dataset is only showing "Pseudochromosome_1" and "Pseudochromosome_2"...when I have 33 chromosomes in my dataset. How can I convert all 33 chromosomes instead of Pseudo 1 and 2? ...
written 20 days ago by offspring182130
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pseudochromosomes in VCFtools
... Hi everybody, I am trying to study individual chromosomes in my dataset, and create a plink file in vcftools with a single chromosome. However the chromosomes are labeled as Pseudochromosome_1, 2, 3, etc. Thus, when I enter the command: vcftools --vcf filename.vcf --plink --chr 1 --out filename ...
genome written 4 weeks ago by offspring182130 • updated 4 weeks ago by chrchang5234.9k
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Answer: A: ls function in windows bash terminal not showing all files
... I figured it out, thanks everybody! Some of my files didn't have permission. So I used the ls -a to find out which files those were, then used sudo chmod 777 filename to enable access to them via terminal. ...
written 4 weeks ago by offspring182130
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ls function in windows bash terminal not showing all files
... I am pretty new to bioinformatics, and just installed bash and ubuntu on my PC. When I use the 'ls' command for my home directory, it shows only a few of the files and folders. It also neglects to show my genome vcf file. Terminal also does not recognize that there is a vcf file present when i try t ...
genome written 5 weeks ago by offspring182130

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Scholar 4 weeks ago, created an answer that has been accepted. For A: ls function in windows bash terminal not showing all files

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