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miriam.mueller
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@miriammueller-21440
Last seen 5.4 years ago
Hello,
I am working with DESeq2-result files (.csv) in a bioinformatic context.
I wonder, if there is a convention on how the "features" are named for DESeq2 csv outputs.
In one of my sample datasets for genes for example, genes are named with "geneName.gene". Would an example for CDS be named "cdsName.cds"? Is the .gene an error and the name column would normally contain only the feature name?
Thanks in advance,
Miriam
So, I have also investigated the count files of that dataset, which troubles me. The genes are named identically (name.gene).
Am I right, that upon running DESeq2 with e.g. those count data, one specifies how the data is read in (haven't used DESeq2 myself, read the docu and examples though) and then DESeq2 takes the "names" or identifiers the user specified? (which actually could be anything, when disregarding biological sense)
What's the question exactly? DESeq2 takes count matrices as input (or other various files described in the docs). It doesn't matter to DESeq2 what the rows are named. Is there a question about how to use DESeq2 or what gene names are most common? The latter you can try posting to a general bioinformatics forum such as Biostars. Here you can post specific software questions.
This answered my question. There is "no" convention for row names. It depends on the input and I wasn't sure about that and wanted clarification. Thanks :)