User: jingjin2203

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jingjin220330
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Posts by jingjin2203

<prev • 22 results • page 1 of 3 • next >
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Comment: C: filtering SNPs by samples?
... It actually worked when I tried "GEN[0].GT=='1/1'" instead of using sample name! I guess I will go with that. Sorry for keeping bugging you, I just had another question. Does the 0 in GEN[0] refer to the first sample in VCF file? In my case, I have 12 samples, so I would put GEN[0] to GEN[11] in the ...
written 2 days ago by jingjin220330
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Comment: C: filtering SNPs by samples?
... Hi guillaume.rbt, thank you for your kind reply!! After modifying the code, I had the same error as I posted above. I am not aware of anything wrong in the header of my vcf file. I attached a small section of my vcf file, it would be great if you could help me take a look at it. Thanks again! ##f ...
written 4 days ago by jingjin220330
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Comment: C: filtering SNPs by samples?
... Thanks a lot! Really appreciated it! I am currently trying your recommendation, but having some trouble. Hope you could further help me out. 1. The SnpSift manual says I can create an expression using sample names instead of genotype numbers, so I put sample1name in GEN[], am I doing it right? 2. ...
written 7 days ago by jingjin220330
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filtering SNPs by samples?
... Hi all, I have a bcf file containing SNPs called across 12 different samples. I am specifically interested in the SNPs that occurred in the first 6 samples but are absent in the second 6 samples. I was wondering if there is any tool that would allow me to do this? Any help is appreciated! Thanks ...
bcftools snp sequencing written 7 days ago by jingjin220330 • updated 7 days ago by guillaume.rbt560
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Comment: C: error while making a DegList object on R using edgeR package (Error in colSums(c
... I realized the numbers in my matrix were characters. It looks like I have fixed it by class(rawCountTable) <- "numeric" Thanks!! ...
written 14 days ago by jingjin220330
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Comment: C: error while making a DegList object on R using edgeR package (Error in colSums(c
... Hi Gordon, I had the same problem and I tried to fix it following your post here. However, edgeR still gave the error message. Here is the code I used rawCountTable <- read.delim("featureCount_counts", header = FALSE, sep = "\t", row.names = 1) rawCountTable <- rawCountTable[-c(1,2) ...
written 14 days ago by jingjin220330
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Comment: C: Unequally pooling libraries for RNAseq?
... Thank you for your suggestion! I would definitely check it out when I get my data back. ...
written 3 months ago by jingjin220330
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Comment: C: Unequally pooling libraries for RNAseq?
... Good point! I am looking at the gene expression after fungus-plant interaction. But I'm specifically interested in the fungal side. ...
written 3 months ago by jingjin220330
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Comment: C: RNA-seq, why normalize for library size?
... Hi Bastien, Thanks a lot!! I'll definitely take a look at the DEseq2 vignette document you recommended. It looks like gene length and RNA population composition won't be a problem for me. ...
written 3 months ago by jingjin220330
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Unequally pooling libraries for RNAseq?
... Hi everyone, I have a question about pooling libraries for RNAseq. I'll really appreciate it if you could comment on this. I have 12 samples that I would like to run RNAseq with. The 12 samples were collected from 2 different fungal cultures under 2 different conditions, and 3 replications under ...
deseq rna-seq sequencing written 3 months ago by jingjin220330 • updated 3 months ago by shawn.w.foley550

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