create index for genome instead of transcriptome using Salmon
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3 months ago
Sara ▴ 200

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?

salmon • 901 views
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For my analysis I need to use genome

Can you explain? salmon is not designed for use with genomes (though it does use genome sequence as a decoy).

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Why would you use salmon for a genome alignment?

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