User: fatimarasool135

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Posts by fatimarasool135

<prev • 102 results • page 1 of 11 • next >
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Comment: C: gene sequence fetching from bam or fastq file of rna seq data
... Hi Buffo, Thank you.I have the gene sequences now.but these are the same sequence as present in database. After sequence alignment i did not any variation in six samples of target gene. why it is same? ...
written 3 days ago by fatimarasool13540
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Comment: C: edgeR dispersion value (common BCV (square- root-dispersion)) when no replicates
... Hi ATpoint, I have read vst in the manual of DEseq2. but i could not understand itkindly write command I have compared the samples to each other by using the Deseq2 tool and have list of genes with parameters generated by deseq2 tool. Now i have no chance to take biological replicates. You have tol ...
written 3 days ago by fatimarasool13540
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edgeR dispersion value (common BCV (square- root-dispersion)) when no replicates in dataset
... I am performing several analysis of differential expression (using edgeR). Reading edgeR manual I am not sure about BCV value that I should use. I am comparing libraries of the same species (non model species) and i have no biological replicates. In the manual you say that "Typical values for the ...
software error R next-gen rna-seq genome written 3 days ago by fatimarasool13540
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Comment: A: biomaRt: Cannot access the zebra fish dataset
... Hi Mike Smith, I am using the biomart package. and i have not seen dataset of wheat. Can you please tell me how to acess the wheat dataset ? ...
written 6 days ago by fatimarasool13540
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wheat_gene_ensembl not available on biomaRt
... Hi , I have the STRG gene ids.I want to get the gene names of these genes or ensembl gene ids of wheat . How can I get It? I have read the Biomart package but fond nothing. ...
genome assembly rna-seq gene written 8 days ago by fatimarasool13540
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Comment: A: How to run the Deseq2 tool wothout replicates.
... Yes i have no replicates in any group and i nothing found answer to my question in manual of Deseq ...
written 8 days ago by fatimarasool13540
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Comment: C: How to run the Deseq2 tool wothout replicates.
... Yes i have no replicates in any group and i nothing found answer to my question in manual of Deseq ...
written 8 days ago by fatimarasool13540
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How to run the Deseq2 tool without replicates.
... Hi, I am doing differential gene expression by Deseq2 tool. I have no replicates and I am doing multi group comparison between samples. Can anyone tell me how to run the Deseq2 tool without replicates? ...
R bioconductor deseq2 rna-seq written 8 days ago by fatimarasool13540 • updated 8 days ago by waqaskhokhar99970
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Comment: C: how to set Deseq factor
... I am trying to create the coldata frame for DESeqDataSetFromMatrix design to instantiate the DESeqDataSet, by using the following command (coldata <- data.frame(row.names=colnames(countdata), condition))` but i got this error >> coldata <- data.frame(row.names=colnames(countData) ...
written 10 days ago by fatimarasool13540
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Comment: C: how to set Deseq factor
... Can you please help me more... can you set the script according to my dataset .? ...
written 11 days ago by fatimarasool13540

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