I am having issue with
salmon index formation since I cannot use
STAR due to limited amount of RAM (as per my recent post). I tried to follow this tutorial on how to create decoy-aware transcriptome as well as doing directly this and I have few question.
1) how much memory is required to build index and do the alignment with salmon?
2) is it necessary to build a decoy-aware transcriptome file? because according to the manual it is recommended.
Now salmon seems to be frozen (it has been > 2 hrs trying to generate decoy-aware transcriptome for human. is this time normal? The code is really simple and follows the tutorial:
mkdir test cd test wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz grep "^>" <(gunzip -c GRCh38.primary_assembly.genome.fa.gz) | cut -d " " -f 1 > decoys.txt sed -i.bak -e 's/>//g' decoys.txt cat gencode.v44.transcripts.fa.gz GRCh38.primary_assembly.genome.fa.gz > gentrome.fa.gz salmon index -t gentrome.fa.gz -d decoys.txt -p 12 -i human_index --gencode
but what I get is .
is this normal? how long does it take to be human index usually? is there anything I can do? my computer is a Mac M1 16G RAM.
I also tried downloading the transcriptome and then do it
salmon index -t human.fa.gz -i human_index and it is still stuck at the same level.
if I do
top both code are still running
Thank you very much