Entering edit mode
5.1 years ago
ang.dionysos.gao
•
0
Hi I have RNA seq data from black 6 mice cells. I want to link the sequence data to the proteins of the mice. More precisely I want to know the protein expression level of these mice cells. Are there any computational tools that do it?
If you want protein quantification then RNA-seq is not the right experiment. Proteomics (mass spec) would be the way to go. No computational tool can fix that.
Thx. I just want to have a very rough sense about what proteins are expressed.
Alright, that would work. In which format is your data? You were not very specific about that.
There are many pipelines that can do the analysis, and if you want to create a custom pipeline you can check out Galaxy website.
Moved to comment as it does not add any valuable details. Please make a suggestion for a pipeline you think is suitable rather than linking Galaxy itself which is a platform rather than a specific pipeline.
Not an expert in this but I think there is little and no reliable correlation between RNA levels and protein abundance due to posttranscriptional regulation and other biological processes making thing complicated, see What Is The Relationship Between Rna And Protein Levels In Vivo? RNA-seq is simply the wrong approach here.
I think you can use Tuxedo suite can be use to analyze RNA Seq data. Tuxedo suite includes: Bowtie, tophat, cufflinks , these can be also implement using Galaxy platform if you are not familiar with command line tools.
Now there are new tools that can be included as well, which HISAT2-Stringtie and Ballgown as well.
Moved again to comment. OP is asking about inference of PROTEIN levels from RNA-seq data. You are suggesting a (deprecated) RNA-seq lowlevel pipeline.
thanks for the link. very informative