User: boymin2020

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boymin202020
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Posts by boymin2020

<prev • 30 results • page 1 of 3 • next >
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Input for -w options of smartpca.perl
... Hi, I am doing SNP-array data QC with Anderson's paper on nature protocol.https://www.nature.com/articles/nprot.2010.116 However, its supplement data cannot be downloaded now which make me confused about a file named "pca-populations.txt". It will be very appreciated if anyone can give a copy of th ...
smartpca written 4 days ago by boymin202020
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Questions about gene length and GC content in CQN normaliztion
... Hi, There are several questions after I read the manual of CQN normalization method. Although I also have checked several related posts of Biostar, but still confused a lot. 1. How to get the information of gene length? I think it is easy to calculate as the gene bands can be obtained directly fro ...
gc content cqn rna-seq gene length written 3 months ago by boymin202020 • updated 5 weeks ago by rrbutleriii50
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Comment: C: Question about the reliability of --check-sex in PLINK2
... Thank you very much. ...
written 6 months ago by boymin202020
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Comment: C: Question about the reliability of --check-sex in PLINK2
... 1. Use --freq to get the MAF report, then extract variants (>0.01) with rs outside of PAR? ...
written 6 months ago by boymin202020
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Comment: C: Question about the reliability of --check-sex in PLINK2
... Thanks for your reply. Another two questions. 1. How the select the specific set of SNPs? 2. What is the meaning of PAR? ...
written 6 months ago by boymin202020 • updated 6 months ago by RamRS20k
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Question about the reliability of --check-sex in PLINK2
... Hi all, I have tried to use plink2 to check the gender situation of my several datasets. It always shows more problem samples than expected. For some datasets, I also have RNAseq data. Then I checked again with some genes just on chromosome X or Y. It turned out a few problem samples. Therefore, I ...
plink2 sex-check written 6 months ago by boymin202020 • updated 6 months ago by chrchang5234.8k
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Comment: C: Chromosome lost after merge with vcf-merge
... Yes. Thanks for the follow-up. ...
written 7 months ago by boymin202020
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Comment: C: Chromosome lost after merge with vcf-merge
... Thanks for your advice. **bcftools merge** works much faster and very well. ...
written 7 months ago by boymin202020
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Chromosome lost after merge with vcf-merge
... Hi all, I have merged a number of WGS VCF files generated from the standard GATK pipeline with vcf-merge function of VCFtools. The merged big VCF file shows that the chromosomes after 19 (e.g., Chrom20) lost. I guess one/some individual VCF files do(es) not have the lost chroms. Are there any possi ...
vcf-merge written 7 months ago by boymin202020
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DE heatmap before or after limma adjustment
... Hi, I have a proteomics data from MaxQuant software. According to the manual, the data has been normalized by the MaxQuant internal method. After cleanup, QC and imputation (**imputation data**), I have done the adjustment with limma for AOD, Sex and PMI (**residual data**). In the next step, I wa ...
de heapmap limma written 8 months ago by boymin202020 • updated 7 months ago by Devon Ryan88k

Latest awards to boymin2020

Supporter 3 months ago, voted at least 25 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For Java memory issue in GATK
Popular Question 5 months ago, created a question with more than 1,000 views. For Memory usage of picard Samsort

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