User: jingjin2203

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jingjin220340
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Posts by jingjin2203

<prev • 34 results • page 2 of 4 • next >
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Comment: C: RNAseq raw read counts for measuring relative gene expression?
... Thank you for your comments! I was directed to this post https://www.researchgate.net/post/Is_it_scientifically_accepted_to_compare_RNA-Seq_data_to_RTqPCR_data/amp It was mentioned that " *Library mass normalization is performed using a different set of methods of which TMM is currently hands down t ...
written 14 months ago by jingjin220340
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RNAseq raw read counts for measuring relative gene expression?
... Hi All, I have a raw read count file of RNAseq normalized using TMM in edgeR. In addition to finding DEGs using edgeR, I was wondering if it is valid to compare the number of reads mapped to the gene of interest and the number of reads mapped to 'internal control' (eg. ubiquitin conjugating enzyme) ...
gene rt-pcr rna-seq written 14 months ago by jingjin220340 • updated 14 months ago by darbinator220
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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 14 months ago by jingjin220340
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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 14 months ago by jingjin220340
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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 14 months ago by jingjin220340
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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 14 months ago by jingjin220340 • updated 14 months ago by guillaume.rbt800
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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 15 months ago by jingjin220340
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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 15 months ago by jingjin220340
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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 18 months ago by jingjin220340
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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 18 months ago by jingjin220340

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Popular Question 14 months ago, created a question with more than 1,000 views. For individual inbreeding coefficient (vcftools -het)

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