User: microbiotaiota

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Posts by microbiotaiota

<prev • 30 results • page 3 of 3 • next >
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Comment: C: Create table of gene expression for multiple samples
... Thanks, I'll give it a crack ...
written 3 months ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... Thank you! I have given it a try, however I have run into 2 issues. Firstly, when running the below I get `duplicate 'row.names' are not allowed` and I think the this comes down to `row.names=1`. I checked the files to see if there were any duplicate Gene IDs and there weren't (`cat file.tab | cut ...
written 3 months ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... I have both, I thought that having each file in the same directory might make it easier. I'll be sure to clarify in future posts. ...
written 3 months ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... Thank you, fixed it up now ...
written 3 months ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... Hopefully it is clear, there aren't commas in the real file, added them to make it a bit more clearer. By expressed the PI wants anything 0 and above (so all genes, sorry for the confusion). ...
written 3 months ago by microbiotaiota20
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Comment: C: Create table of gene expression for multiple samples
... I have geneabundance.tab and .gtf files from stringtie (updated in original post) ...
written 3 months ago by microbiotaiota20
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Create table of gene expression for multiple samples
... I have 60 samples and my PI wants a table (excel spreadsheet) containing all expressed genes in 60 samples. I have used hisat and stringtie. I don't know how to create such a table unless I code something and my coding skills are rudimentary. Or that I manually extract the expression values and past ...
hisat stringtie rna-seq written 3 months ago by microbiotaiota20 • updated 3 months ago by Kevin Blighe67k
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Comment: C: Uneven number of technical replicates for biological replicates in RNA-seq
... Thank you. this was confusing me ...
written 4 months ago by microbiotaiota20
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Comment: C: Uneven number of technical replicates for biological replicates in RNA-seq
... Thank you, I'll go ahead and concatenate the files. ...
written 4 months ago by microbiotaiota20
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Uneven number of technical replicates for biological replicates in RNA-seq
... Hi everyone, I am new to RNA-seq analysis and I'm trying to understand what to do with my data. I have 60 biological samples (30 control and 30 diseased, paired samples). Each biological sample has 1 or two technical replicates. I will concatenate the .fastqc files for technical replicates to yield ...
technical_replicates rna-seq written 4 months ago by microbiotaiota20 • updated 4 months ago by Ido Tamir5.1k

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