In Salmon's documentation, they state you can provide multiple read files when "one may wish to quantify multiple replicates or samples together, treating them as if they are one library." If, for example, you input 2 separate fasta files from the same sample (collected on separate days) will the output will be as if you submitted only 1 sample? Or am I interpreting this incorrectly?
How can the same sample be collected on separate days? Did you prepare a biological replicate on separate days?
Yes, apologies. Same sample source (same animal) but collected twice on two separate days, exposed to different conditions on each day.
Thanks for clarifying.
hi,
I am investigating the same question at the moment: my input is -1 replica1_read1 replica2_read1 replica3_read1 -2 replica1_read2 replica2_read2 replica3_read2 and I got :
From the documentation:
So your output is correct. Unfortunately, I think your best bet is to run 3 individual commands which IMO is good practice especially if you want to switch into parallelization.
yeah, I figured the same. tnx for the confirmation :)