dynast.ref
Module Contents
Functions
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Generate a STAR index from a reference. |
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- dynast.ref.STAR_genomeGenerate(fasta_path, gtf_path, index_dir, n_threads=8, memory=16 * 1024 ** 3, temp_dir=None)
Generate a STAR index from a reference.
- Parameters
fasta_path (str) – path to genome fasta
gtf_path (str) – path to GTF annotation
index_dir (str) – path to output STAR index
n_threads (int, optional) – number of threads, defaults to 8
memory (int, optional) – suggested memory to use (this is not guaranteed), in bytes, defaults to 16 * 1024**3
temp_dir (str, optional) – temporary directory, defaults to None
- Returns
dictionary of generated index
- Return type
dictionary
- dynast.ref.ref(fasta_path, gtf_path, index_dir, n_threads=8, memory=16 * 1024 ** 3, temp_dir=None)