User: bioinforesearchquestions

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Posts by bioinforesearchquestions

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Is there any other options to fetch the rs-ids for the markers for the Illumina custom array?
... Hi, I would like to get rs-ids for the markers in the Illumina custom arrays used for iScan platform. Some of the markers have already annotated with rs-ids. But most of them are not. The list is very big, so I cannot manually check them one by one in dbsnp. Is there any other options for me to fe ...
illumina iscan dbsnp snp rsids written 16 days ago by bioinforesearchquestions200
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(Closed) How to identify the pathways that are enriched in up-regulated and downregulated genes from RNAseq?
... Hi friends, Which approach is correct to do GSEA and pathway analyses. - considering all ~20,000 genes as the input for Broad's GSEA tool or - considering only the significantly (p.adj < 0.05) differentially expressed genes as the input for Broad's GSEA tool My aim is to identify the pathwa ...
degs pathway analysis rna-seq gsea written 6 weeks ago by bioinforesearchquestions200
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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 10 weeks 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 10 weeks 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 10 weeks 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 10 weeks ago by bioinforesearchquestions200 • updated 10 weeks ago by i.sudbery4.3k
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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 4 months 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 4 months 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 4 months ago by bioinforesearchquestions200

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