create index for genome instead of transcriptome using Salmon
I am trying to create index using salmon for human Genome (not transcriptome). The version of salmon I am using is : salmon v0.13.1 .
The command I used is :
salmon index \
-t /hg38_genome/GRCh38.p13.genome.fa \
-i index
The main error I am getting is:
Command error:
[2022-01-26 12:20:19.647] [jointLog] [warning] Entry with header [KI270896.1] was longer than 200000 nucleotides. Are you certain that we are indexing a transcriptome and not a genome?
If I use transcriptome file instead of genome, it works perfectly and returns the index files. I got both transcriptome and genome from the gencode.
For my analysis I need to use genome. do you know how I can use genome?
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Can you explain?
salmonis not designed for use with genomes (though it does use genome sequence as a decoy).Why would you use salmon for a genome alignment?