I am trying to run Salmon locally on prostate cancer samples, and I used this command:
salmon quant -i data/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index/default -l A -1 SRR21898893_1.fastq.gz -2 SRR21898893_2.fastq.gz --validateMappings --gcBias -o transcripts_quant
I downloaded the pre-built versions of the partial decoy (salmon_partial_sa_index) and full decoy (salmon_sa_index) indices from on refgenie following the Salmon documentation.
I tried first running the command with the full decoy index getting the error:
Exception : [std::bad_alloc] probably due to a memory problem (my macbook has 16GB and the salmon_sa_index weighs 18GB) and then running the command with the partial decoy index getting my counts successfully.
My question is, what exactly is the difference and how much do the results differ using the two indexes? Also, what flags should I use besides -gcc?