miRcounts

This script will take raw small RNA reads in fastq format and output counts of the known miRNA. This script requires Python V2, Biopython, and Blast+.

usage: ./raw_to_counts.py known_miRNA.fasta RawReads.fastq output.txt

Test files:

known_miRNA.fasta

A set of known Brassica napus miRNA from the publication: (identical miRNA sequences were removed)

Shen, Enhui et al. "Identification, Evolution, And Expression Partitioning Of miRNAs In 
Allopolyploid Brassica napus". EXBOTJ 66.22 (2015): 7241-7253.

RawReads.fastq

Sequence reads in fastq format from a Brassica napus sample, taken directly from a MiSeq. No pre-processing required -- just be sure to unzip them first, can be done in the command line with this command: gunzip filename.fastq.gz

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This project is licensed under the terms of the MIT license.