Data Quantification : cDNA / Transcriptome Database Index Generation
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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