How does the ‘Generate gene to transcript map’ tool produces the file containing correspondence between gene ids and transcript ids based on the names of DE NOVO transcripts assembled by rnaSPAdes? The reference genome is not available.
Kamran Azim
Hello @kamran.azim
This tool does not interpret rnaSPADes assemblies.
If you do not have a reference genome, you can explore tools like Kallisto and Salmon for expression analysis using your transcriptome.
Some ideas about how to do this are discussed in the Bioconductor vignettes with more guidance at their forum here: https://support.bioconductor.org/post/search/?query=transcriptome+expression+analysis
Hope this helps! 