-------------  miRDeep  -------------


# Reads download: we already have it
# wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR158/006/SRR1586016/SRR1586016.fastq.gz
# gunzip SRR1586016.fastq.gz


# Downloading the genome: we already have it
# wget ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz
# gunzip Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz

# Building a genome index: we already have it
# bowtie-build Homo_sapiens.GRCh38.dna.chromosome.22.fa index/chr22


# mapping the reads
mapper.pl SRR1586016.fastq -e -h -j -k TGGAATTCTCGGGTGCCAAGG -l 18 -m -p index/chr22 -s SRR1586016_collapsed.fa  -t SRR1586016_collapsed_vs_genome.arf –v


# downloading mature miRNAs from miRBase: we already have it
# wget ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz
# gunzip mature.fa.gz


# editing the genome
nano Homo_sapiens.GRCh38.dna.chromosome.22.fa


# miRNA search
miRDeep2.pl SRR1586016_collapsed.fa Homo_sapiens.GRCh38.dna.chromosome.22.fa SRR1586016_collapsed_vs_genome.arf mature_mirbase_human.fa mature.fa premirna_mirbase_human.fa -t human 2> report.log





-----------------  Mapping sRNA-Seq reads and visualization  -----------------



# building a Bowtie index
bowtie-build precursors.fasta index/precursors


# mapping
bowtie -t -p 2 -v 0 -a -f index/precursors SRR1586016_nonredundant.fasta SRR1586016.out


# visualizing
python alignment.py SRR1586016.out precursors.fasta # ----> SRR1586016.out.html


