User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Comment: C: Pathway analysis and Gene enrichment Analysis Queries
... Thanks, Jared. I have done GSEA on all three. But I was not sure which one is more meaningfull in interpreting. For instance, when I did GSEA on upregulated gene list (570 genes). I selected this GENESET DATABASE "Mouse_GOBP_AllPathways_no_GO_iea_October_01_2018_symbol.gmt". GSEA finished successfu ...
written 11 days ago by bioinforesearchquestions190
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Comment: C: Pathway analysis and Gene enrichment Analysis Queries
... Hi Kevin, Sample1 - Mutant, Sample2 -Wildtype. As per the list given to me there are 680 genes in that cuffdiff output file. Just for understanding, when I took log2(Value_2/Value_1) -> Wildtype/Mutant, I got the same logFC as per the cuffdiff output. As you mentioned, I categorized the genes b ...
written 11 days ago by bioinforesearchquestions190
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Pathway analysis and Gene enrichment Analysis Queries
... Hi All, I am working on the RNAseq samples. Planning to do pathway analysis and gene enrichment analysis. As of now don't have much background on these analyses. Currently doing some background research. If you people know some useful resources, kindly do share with me. - At first instance, why do ...
rnaseq enrichment score pathway analysis gsea written 12 days ago by bioinforesearchquestions190 • updated 11 days ago by dz235350
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Comment: C: mirdeep2 v 10
... Can you check the config.txt file? It should be in the below format (make sure, you provide space in between fastq file and sample name) Sample1.fastq Sample1 Sample2.fastq Sample2 Sample3.fastq Sample3 ...
written 27 days ago by bioinforesearchquestions190 • updated 26 days ago by RamRS19k
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Comment: C: cummeRbund create database ERROR
... Have you figured out what is the issue with this cummeRbund? Even I am getting 0 for cuff object. ...
written 27 days ago by bioinforesearchquestions190
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Comment: C: Error in cummeRbund R library package (Error: Columns index not found)
... > packageVersion("cummeRbund") [1] ‘2.16.0 ...
written 27 days ago by bioinforesearchquestions190
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How to download VCF of 1000 genome project with population frequencies?
... Hi folks, I would like to grab the population frequencies for a list of SNPs from 1000 genome project (https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/ ). Currently, I am searching one snp at a time and downloading as a VCF. Is there a way for me to search my list and get the entire popul ...
vcf rsids snps 1000genome written 7 weeks ago by bioinforesearchquestions190 • updated 7 weeks ago by finswimmer8.1k
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Comment: C: Error in cummeRbund R library package (Error: Columns index not found)
... Yeah, tried without that as well. Same error and empty cuffset instance. ...
written 10 weeks ago by bioinforesearchquestions190
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Error in cummeRbund R library package (Error: Columns index not found)
... Hi, With the below cuffdiff output, I already generated plots using cummeRbund package. But now, I am getting some error. What could be the reason? Have anyone faced it before? cuff_data <- readCufflinks("/Users/admin/Desktop/RNA_seq_Analysis/cuffdiff", rebuild = T) Creating databa ...
rnaseq cummerbund cuffdiff written 10 weeks ago by bioinforesearchquestions190 • updated 10 weeks ago by genomax59k
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Comment: C: What is the appropriate assembler for PacBio long reads
... As of now, I have been told that I am going to get only the PacBio long reads. Why do you say that I should get some Illumina? ...
written 4 months ago by bioinforesearchquestions190

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