User: Nicholas Owen

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Posts by Nicholas Owen

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Comment: C: DESeq2 time series tissue specific differences over time
... Thank you Gavin for taking the time to reply - I appreciate your insight. Apologies for the delay in response, I have been getting my head around things a little more. I wanted to clarify though, but you mentioned the summands should correspond to things in the resultsNames, could you elaborate a li ...
written 4 months ago by Nicholas Owen0
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Comment: A: DESeq2 time series tissue specific differences over time
... Thank you Gavin for taking the time to reply - I appreciate your insight. (snipped as comment moved to under Gavin's post) sorry. ...
written 4 months ago by Nicholas Owen0
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DESeq2 time series tissue specific differences over time
... Hi all, I have an RNA-seq data set of samples that I wish to use for analysis of differential expression with DESeq2. The data has three time points; 1 day, 5 day and 10 days with two different tissue samples taken from each time point (Tissue A, reference and Tissue B), 7 replicates of each. Ini ...
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Comment: C: ensembldb salmon deseq2 txt2import right tool?
... I have just started a zebrafish project, will you be creating and EnsDbs for Ensembl v89 of Danio rerio as well, if not may I ask the best way to? Thanks ...
written 5 months ago by Nicholas Owen0
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Comment: C: DESeq2 output with multiple Ensembl Gene Names per row, how to resolve?
... Thanks for the information, appreciate it. From the sorted BAM we have removed the marked duplicates using samtools view -F 0x0400 and piped this into the dexseq count.py to get the counts for each sample, then prepared the matrix from this data. I can see that output has the multiple ENSG per line ...
written 6 months ago by Nicholas Owen0
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DESeq2 output with multiple Ensembl Gene Names per row, how to resolve?
... Dear All, We have been using DESeq2 on our RNA-seq data to look for differential expression of genes and it works well. One issue that keeps on cropping up is the allocation of the EnsemblIDs per row in results(dds), frequently we are getting multiple IDs per row, for example: ENSG00000001084+EN ...
rnaseq deseq2 ensembl written 6 months ago by Nicholas Owen0 • updated 6 months ago by Michael Love14k

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