User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Comment: C: Selecting methods for performing pairwise RNAseq analysis without replicates
... Sure, I will do it as you recommended for tissue 1 and tissue2. Am I correct? > Metadata > Sample Tissue Genotype >Sample1 Tissue1 Wildtype >Sample2 Tissue2 Wildtype >Sample3 Tissue1 Knockout >Sample4 Tissue2 Knockout Blockquote ...
written 2 days ago by bioinforesearchquestions200
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Comment: C: Selecting methods for performing pairwise RNAseq analysis without replicates
... Thanks, Sudbery. For 2,3,4 pair-wise analyses, even If I do paired t-test for all ~45,000 genes, I will get a single p-value for each pair-wise. How do I get the list of DE genes. ...
written 3 days ago by bioinforesearchquestions200
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Comment: C: Selecting methods for performing pairwise RNAseq analysis without replicates
... Yeah, I already explained to them that pair-wise analyses (2, 3 and 4) without replicates we won't be able to identify DE genes. The p-value which we get is meaningless without replicates. But they are persistently asking me to provide a list of genes based on the log2 fold change values. ...
written 3 days ago by bioinforesearchquestions200
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Selecting methods for performing pairwise RNAseq analysis without replicates
... Hi friends, I need some help in deciding the tools and steps in the following analyses. I got 6 RNAseq samples, there are no replicates among the six samples. These six samples are from three different tissues. Three of them are wild-type (WT) samples and the remaining three of them are knock-out ( ...
tissues deseq2 deseq rna-seq hisat2 written 3 days ago by bioinforesearchquestions200 • updated 3 days ago by i.sudbery3.7k
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Comment: C: Identifying consensus sequence between multiple Arabidopsis genome sequences
... Hi VKKodali, I am trying to find consensus between the list of full genome sequence not against the reference. ...
written 8 weeks ago by bioinforesearchquestions200
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Identifying consensus sequence between multiple Arabidopsis genome sequences
... Dear folks, I have a list of Arabidopsis full genome sequence in FASTA format. I am planning to align against each of them and find - Consensus sequence - Genomes aligned to the consensus sequence with highlighted SNPs, indels and presence-absence variations any suggestions (articles, tutorial, ...
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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 10 weeks ago by bioinforesearchquestions200
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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 10 weeks ago by bioinforesearchquestions200
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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 10 weeks ago by bioinforesearchquestions200 • updated 10 weeks 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 12 weeks ago by bioinforesearchquestions200 • updated 12 weeks ago by RamRS20k

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