User: mbk0asis

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mbk0asis460
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Korea, Republic Of
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Posts by mbk0asis

<prev • 125 results • page 1 of 13 • next >
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Comment: C: gdc-client download: ERROR: Max retries exceeded
... Try 'TCGAbiolinks'! https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html ...
written 7 weeks ago by mbk0asis460
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Comment: C: How to speed up trimming using trim galorer
... Much better! Thanks~ ...
written 7 months ago by mbk0asis460
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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 8 months ago by mbk0asis460
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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 12 months ago by mbk0asis460
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Comment: C: 1000 genome project - difference between "0" and "0|0"
... Thank you! I understood :) ...
written 12 months ago by mbk0asis460
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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 12 months ago by mbk0asis460
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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 12 months ago by mbk0asis460 • updated 12 months ago by Santosh Anand4.9k
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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 12 months ago by mbk0asis460
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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 12 months ago by mbk0asis460
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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 13 months ago by mbk0asis460

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