Name: miRNA_processing
Owner: Science For Life Laboratory
Description: Scripts to process miRNA from trimming through annotation.
Created: 2013-11-27 07:46:14.0
Updated: 2015-03-02 10:52:42.0
Pushed: 2014-06-18 09:46:55.0
Homepage: null
Size: 5173
Language: Python
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Usage:
pipeline.sh
[-r <genome_reference_file> (FASTA)>]
[-g <genome_feature_file (GTF/GFF)>]
[-m <mirbase_file (FASTA)>]
[-o <output_directory>]
[-n <cores>]
[-f (overwrite existing files)]
[-k (keep temp files)]
<sequence_file> [<additional_sequence_files> <will_be_merged> <before_processing>]
Aligns single-read (not paired-end) RNA samples to reference genomes, annotates them, and counts gene frequencies. Also aligns against miRBase. Visualizes read lengths after trimming. More specifically:
bash pipeline.sh \
-r path/to/reference_file.fa \
-g path/to/annotation_file.gff \
-m path/to/miRBase.fa \
-o output_dir/ \
-n 8 \
-f \
-k \
data_file1.fastq data_file2.fq data_file3_fastq