Processing the reference genome using Picard.CreateSequenceDictionary and SAMtools.FastaIndex

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In this video step, we will use the Picard.CreateSequenceDictionary module in GenePattern to build a dictionary for a reference genome.

In GenePattern search or browse for the module "Picard.CreateSequenceDictionary". Click the module to load it.

Leave the rest of the parameters as is and click "Run"; if successful, the module should output a .dict file.

Next we will create an index for the same reference genome that will complement our dictionary file.

Use the module tab to search or browse for the module "SAMtools.FastaIndex".

Again, head to the GenomeSpace tab and click and drag the fasta file to the input field. Provide an output prefix such as "sacCer3_indexed".

Run the job and await its completion.