Kallisto is used for quantifying the gene expression. Kallisto requires an index file of the cDNA or transcriptome FASTA file to rapidly map RNA sequences to genes.
Command: FASTQ > RNA-sequencing quantification > Create kallisto index...
Parameters to set:
- transcriptome_fasta: the cDNA or transcriptome database in FASTA format (unzipped downloaded file !)
- kallisto_installation_folder
- Use the button Start Kallisto create index to create the index file
- Use the "Resource Monitor" application to monitor computer activity
Results:
The cDNA database index file (.idx):
Comments: matthias.wilm@ucd.ie
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