User: mbk0asis

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mbk0asis420
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Korea, Republic Of
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Posts by mbk0asis

<prev • 124 results • page 1 of 13 • next >
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Comment: C: How to speed up trimming using trim galorer
... Much better! Thanks~ ...
written 4 months ago by mbk0asis420
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Answer: A: How to speed up trimming using trim galorer
... Use GNU Parallel! Your 'for-loop' code processes one sample at a time. (it waits until one sample is finished and starts next.) Use 'parallel' to process multiple samples simultaneously! If you have reads like this; sample1.R1.fq.gz sample1.R2.fq.gz sample2.R1.fq.gz sample2.R2.f ...
written 4 months ago by mbk0asis420
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Comment: C: How to calculate read frequency from read counts for each gene in all samples al
... I'm not sure what exactly you want, but I assume you don't know how to fix a field using '$' sign. If so, check this cite. [https://www.excel-easy.com/functions/cell-references.html][1] But excel is not efficient to handle a larger dataset. Use R or something similar. They are much better! [1]: ...
written 9 months ago by mbk0asis420
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Comment: C: 1000 genome project - difference between "0" and "0|0"
... Thank you! I understood :) ...
written 9 months ago by mbk0asis420
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Comment: C: 1000 genome project - difference between "0" and "0|0"
... So, "0" = males, "0|0" = females for chrX genes? ...
written 9 months ago by mbk0asis420
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1000 genome project - difference between "0" and "0|0"
... Hi, all! I'm analyzing variants in a gene of interest and found some variants were denoted as "0" or "0|0" by samples. I'm guessing "0" would mean no sequencing while "0|0" indicates homozygous WT. Am I on the right track? What are those marks mean? Thank you! ...
vcf genotype 1000 genome project written 9 months ago by mbk0asis420 • updated 9 months ago by Santosh Anand4.8k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... I thought I should avoid to use plink2 since they said it was in beta testing on the old home page, and missed your note on the top. Thank you! ...
written 9 months ago by mbk0asis420
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format
... I'm getting an error message saying the options entered were unused options. Any idea what went wrong? The command I used and the result are below. Thank you! $ plink --noweb --bcf ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz.bcf --keep-allele-order --vcf-idspa ...
written 9 months ago by mbk0asis420
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Comment: C: Can I obtain data of individula's called variants from 1000 genome project?
... Opps! How did I miss that? Thank you, Kevin! ...
written 10 months ago by mbk0asis420
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(Closed) Can I obtain data of individula's called variants from 1000 genome project?
... Hi. As mentioned in the title, I'd like to obtain the Exome-seq data from the 1000 genome project in VCF. But I couldn't find them. VCF files I found seemed to have the combined variant data. Am I missing something here? Or they just don't have the variant called data of individuals? Thank y ...
vcf 1000 genome exome-seq written 10 months ago by mbk0asis420

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