Hi,
I'm trying to run sleuth to look for differential gene expression between two conditions, but I find the manual a bit hard to interpret.
After running kallisto I have extensions in the transcript IDs (like "ENST00000632859.1") and I assume that's why I cannot get the output data mapped to gene IDs while running biomaRt as described in the "getting started" webpage, anyone knows how to deal with this? Can I just remove the extensions in the .tsv file or do I need to change something in the bootstrap file as well?
Did you use their transcriptome index? Because that one gives me nicely formatted name, causing no problem to map them to the gene names.
I used a fasta file for the human genome looking like this:
Maybe I should try rebuild my index and rerun kallisto...
These are the transcriptomes they suggest to use: http://bio.math.berkeley.edu/kallisto/transcriptomes/