create index for genome instead of transcriptome using Salmon
0
0
Entering edit mode
2.9 years ago
Sara ▴ 260

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 • 1.7k views
ADD COMMENT
0
Entering edit mode

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).

ADD REPLY
0
Entering edit mode

Why would you use salmon for a genome alignment?

ADD REPLY

Login before adding your answer.

Traffic: 2207 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6