User: vw

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vw20
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1 year, 1 month ago
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y********@marquette.edu

Posts by vw

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Hot to retrieval a SNP from a very big vcf file by position with tabix
... I figure out the issue: In the source vcf file, the content in the chromosome column is a plant number without prefix "chr". So, my command line should be: tabix source.vcf.gz "1:10019-10019" It works well now. Thank you so much! ...
written 16 days ago by vw20
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Comment: C: Hot to retrieval a SNP from a very big vcf file by position with tabix
... Thanks for your response. I have compressed and indexed the vcf file. A few first lines of the source.vcf.gz appear as below: gzip -cd source.vcf.gz | head -60 | tail -4 #CHROM POS ID REF ALT QUAL FILTER INFO 1 10019 rs775809821 TA T . ...
written 16 days ago by vw20
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Hot to retrieval a SNP from a very big vcf file by position with tabix
... Hi all, I want to retrieval SNPs in a very large vcf file. I stored the chromosome and position of my interested SNPs in a temp file as below: chr1 2487663 rs2227312 C A 100.0 PASS DP=1825;ASP=true;CAF=0.4008,0.5992;COMMON=1;G5=true;G5A=true;GENEINFO=LOC115110:11511 ...
vcf tabix vcftools snp written 16 days ago by vw20
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Comment: C: Does is make sense if I select a subset from the count matrix to do DE analysis?
... After I approved all genes rather than a subset, the results from DESeq2 and Limma are very similar. Thanks for your help! ...
written 18 days ago by vw20
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Comment: C: Does is make sense if I select a subset from the count matrix to do DE analysis?
... Thanks so much. I also ran the limma+voom on the subset. The result is similar. Is it the same kind of issue? ...
written 19 days ago by vw20
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Comment: C: Does is make sense if I select a subset from the count matrix to do DE analysis?
... Thank you so much! I forgot this point. One more question: I ran the limma + voom on my data also. It generated two similar results respectively. Is that also because of the assumption? ...
written 19 days ago by vw20
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Does is make sense if I select a subset from the count matrix to do DE analysis?
... Hi all, I have a question: I am just interested in a subset (a part of genes) of my raw count matrix. I tried to run DESeq2 with the subset and the complete matrix respectively. However, the DE result based on the subset is very different compared with the corresponding genes in the output based on ...
deseq2 limma rna-seq written 19 days ago by vw20 • updated 19 days ago by Bastien Hervé4.4k
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Comment: C: RNAseq: how to make design matrix for limma
... Thank you so much! You solved my question perfectly. Now I know the meaning of the limma's design matrix. ...
written 20 days ago by vw20
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RNAseq: how to make design matrix for limma
... Hi all, I want to compare the result between limma + voom with DESeq2. But I don't know how to make the design matrix for my date when I am using Limma. I have two groups: WT, ABX. Each group has 6 samples: X1~X6(WT), X7~X12(ABX). It looks like: head(exprSet, n=1) ...
deseq2 limma rna-seq written 23 days ago by vw20 • updated 23 days ago by kristoffer.vittingseerup2.0k
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Comment: C: ATAC-seq DE analysis
... Thank for your reply. Could you please provide your command line? ...
written 24 days ago by vw20

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