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 4 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 4 months ago by jingjin220340 • updated 4 months ago by darbinator190
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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 4 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 5 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 5 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 5 months ago by jingjin220340 • updated 5 months ago by guillaume.rbt650
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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 5 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 5 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 8 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 8 months ago by jingjin220340

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Popular Question 4 months ago, created a question with more than 1,000 views. For individual inbreeding coefficient (vcftools -het)

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