Can we use Gencode Fasta with Salmon?

[philge philip]

Hi

 

Can I use Transcript sequences (Nucleotide sequences of all transcripts on the reference chromosomes) available here https://www.gencodegenes.org/releases/current.html  as input to Salmon?

 

In the Salmon tutorial I read cDNA sequences are used. But I think above sequences are coding+UTR sequences of all transcripts not only mRNA transcripts.

 

Thanks

Philge Philip

[Rob]

Hi Philge,

  Yes, you can absolutely use the transcript sequences provided by Gencode as input to Salmon to build an index.  This will allow Salmon to quantify any indexed transcript, which may be very important depending on the type of analysis you wish to do.  Let me know if you have any other questions.

Best,

Rob