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!
the ncrna in the name could already give you a hint what the file represents - so I would change the file you use. But this is completely independent of the question why you think that two different programs should deliver identical results for a complex task implemented with different assumptions
If you are looking for
transcriptomefile as your title says you should take a look at the files available from GENCODE. There are versions available for all transcripts, protein-coding, long-non coding classes. Look underFasta fileson page linked.I second the comment of Ido, and would like to add, that you probably are looking for the cDNA file from ensembl, which you can find here: mouse cDNA from ensembl version 100. This should work for you.
General FTP download server from Ensembl
Edit: Edited the download file, since genomax pointed out, that you need the transcriptome file