Hello, I am having a trouble with Salmon quant and Kallisto quant. I have used Mus_musculus.GRCm38.ncrna.fa.gz file as the reference transcriptome for both Transcripts fasta file for Salmon quant and Kallisto quant. Even though I was expecting to have an almost identical value with TPM, I ended up getting a different TPM value for both Salmon quant and Kallisto quant. I have no idea which one went wrong, or perhaps both. For other parameters, I have set everything as default. I need a reference transcriptome for mm10 (Mus Musculus) in my RNA-Seq. Where can I find the correct file for reference transcriptome for mm10? (I have read that Ensembl.org and NCBI also offers reference transcriptome, but I just don't know which file to use.
In addition, is there a way I can check if my TPM values are correct (quality check for Salmon or Kallisto?) ?
Thank you so much for helping!