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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
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How do you convert MSTRG.number to Gene name or Gene symbol? #321

Open ghost opened 3 years ago

ghost commented 3 years ago

Dear,

I need to convert MSTRG.number into Gene name or Gene Symbol to be able to run on an R script that allows me to perform differential gene expression analyzes. From what I have been able to understand one method could be with biomaRt the R package, however I am not very practical and therefore I preferred to use the graphical interface, to no avail. Can you help me? If there are also solutions that involve the use of RStudio or R are fine, of course if there was a way to use the graphical interface in this problem we would like it. Thank you

Jacopo

gpertea commented 3 years ago

At the end of the Differential expression analysis section of the StringTie manual there is a note about using the IsoformSwitchAnalyzeR package for something like that, hopefully that can help ?

ghost commented 3 years ago

Sorry for the late reply. I have downloaded IsoformSwitchAnalyzeR however the version of R 4.1 which is required, for the operating system I have, mac os, is unstable. While for windows it seems not to have come out so I couldn't even try with a virtual machine. How can I do it alternatively? Thank you

Jacopo

Il 17/02/2021 17:16 Geo Pertea <notifications@github.com> ha scritto:

At the end of the Differential expression analysis http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#de section of the StringTie manual there is a note about using the IsoformSwitchAnalyzeR https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html package for something like that, hopefully that can help ?

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