User: mbk0asis

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mbk0asis380
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Korea, Republic Of
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Posts by mbk0asis

<prev • 122 results • page 1 of 13 • next >
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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 5 weeks ago by mbk0asis380
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Comment: C: 1000 genome project - difference between "0" and "0|0"
... Thank you! I understood :) ...
written 8 weeks ago by mbk0asis380
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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 8 weeks ago by mbk0asis380
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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 8 weeks ago by mbk0asis380 • updated 8 weeks ago by Santosh Anand4.0k
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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 8 weeks ago by mbk0asis380
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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 8 weeks ago by mbk0asis380
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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 9 weeks ago by mbk0asis380
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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 9 weeks ago by mbk0asis380
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Meaning of mfold upper limit?
... Hi, all! I've been working on ChIP-seq data using 'MACS2', and am confused by "mfold". Does "mfold" represent the relative enrichment against control (IgG or genomic fragments) or background noises in the test sample? And why there's a upper limit in "mfold"? Does that mean fold-enrichment over a ...
mfold macs2 chip-seq written 10 weeks ago by mbk0asis380
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Answer: C: How can I download the fasta file of RepeatMasker UCSC table directly?
... I don't think you can download repetitive sequences directly from UCSC genome browser as genomax mentioned. Instead, get the bed file of RepeatMasker and whole genome sequence of your organism from UCSC genome browser, and use 'bedtools getfasta' to extract the sequences of retroelements. ...
written 11 weeks ago by mbk0asis380

Latest awards to mbk0asis

Popular Question 8 weeks ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 11 weeks ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 3 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 4 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Centurion 4 months ago, created 100 posts.
Popular Question 6 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Popular Question 9 months ago, created a question with more than 1,000 views. For overlapping texts (plot.PCA in FactoMineR)
Scholar 9 months ago, created an answer that has been accepted. For A: select DE genes
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Subsetting DESeq2 results by padj quantity
Student 13 months ago, asked a question with at least 3 up-votes. For Pairwise2 - Biopython - weird local alignment results
Popular Question 13 months ago, created a question with more than 1,000 views. For fasta - reverse complement sequence
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Scholar 15 months ago, created an answer that has been accepted. For A: select DE genes
Popular Question 19 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
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Popular Question 23 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Pairwise2 - Biopython - weird local alignment results
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