I don't understand how to use the row name in this RNA-seq data -- "chr1.10263"
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6 weeks ago
James • 0

I'm trying to use this dataset to look at RNA expression levels in mice. The annotation for each read looks something like this chr1.10263 where the chromosome number is written then followed by a period and then followed by a random five digit number. I can't find anything about it online, and it isn't matching up with any of the Mus.musculus annotations in bioconductor, so I'm at a loss with what to do. If anyone can help, that'd be great. Thanks!

annotation rna-seq bioconductor mus.musculus genetics • 205 views
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Welp. That's a new one for me.

If you wind up getting completely stuck, you can always fetch the fastQs from the SRA (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA837794) and run them through your pseudoaligner of choice for a quick re-quantification of counts.

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