User: rodrigo.nicodemos82

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Posts by rodrigo.nicodemos82

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Comment: C: Why Cuffdiff Output Not Significant?
... The FPKM values for the replicates were: WT_1: 1245.24, WT_2: 874.11 and MUT_1: 0.897, MUT_2: 0.764, MUT_3: 0.823. The third replicate for the WT condition gave very few reads, which is why I didn't include it. I only used two replicates from the MUT condition to compare to the two replicates from t ...
written 3.9 years ago by rodrigo.nicodemos8210
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Why Cuffdiff Output Not Significant?
... Hello,     I am performing RNAseq analysis using TopHat and Cufflinks programs. I have a question for why a gene I am interested is being called Not Significant by Cuffdiff. Here the output for my gene of interest Rh4: gene    sample_1    sample_2    status    value_1    value_2    log2(fold_ch ...
rna-seq written 3.9 years ago by rodrigo.nicodemos8210 • updated 3.7 years ago by Biostar ♦♦ 20
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Comment: C: Cufflinks/Cuffdiff giving incorrect statistics between ON/OFF genes
... Hi Joe, If you scroll to the right in the table you will see that the p_value and q_value for the listed example genes. ...
written 3.9 years ago by rodrigo.nicodemos8210
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Cufflinks/Cuffdiff giving incorrect statistics between ON/OFF genes
... Hello all, I've been using the Tuxedo suite to calculate differential gene expression for Drosophila RNAseq samples I have been analyzing. I've noticed that Cufflinks/Cuffdiff seems to give incorrect statistics between ON and OFF genes. My pipeline for analyzing differential gene expression was: 1 ...
cufflinks cuffdiff rna-seq written 3.9 years ago by rodrigo.nicodemos8210
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Three way comparison RNAseq libraries
... Hello,   I have 3 RNAseq libraries samples with 3 replicates each. I wanted to know what are the RNAseq analysis options for doing a three way comparison? I've seen that DEseq can do differential gene expression analysis for two or more samples. I am also interested in differential isoform expre ...
R analysis rna-seq written 4.0 years ago by rodrigo.nicodemos8210 • updated 4.0 years ago by Steven Lakin1.4k
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Creating Heatmaps with cummeRbund
... Hello, I've been trying to create a heatmap of an RNAseq experiment. I've followed the following online tutorial: https://wikis.utexas.edu/display/bioiteam/Visualization+using+CummeRbund However, when I get to creating the heatmap steps: geneids <- c(up_gene_data$gene_id) myGenes <- getGen ...
R cummerbund rna-seq heatmaps written 4.0 years ago by rodrigo.nicodemos8210 • updated 3.2 years ago by Biostar ♦♦ 20
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(Closed) Bash Script prints out Command
... Hello, I am new to creating bash scripts to run commands. I've tried to run this simple bash script to calculate the genome coverage of a bam file I have using the bedTools genomeCoverageBed command. I am not sure what I am doing wrong, but when I run this script I can a file that contains the prin ...
genome coverage bash written 4.0 years ago by rodrigo.nicodemos8210 • updated 4.0 years ago by Alex Reynolds28k

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