RNAseqScript

#!/bin/sh

# bowtie2, samtools, RepARK and minia need to be installed.
# samtools 1.3 necessary for bam to fasta conversion.


# Run bowtie2-build to index the genome (Given as first argument / $1).
# Run bowtie2 to map the fastQ file (second argument / $2)
# to the indexed genome, and return a SAM file.




echo -e '\n Building genome index... \n'

bowtie2-build $1 indexed-genome


echo -e '\n Aligning reads with genome... \n'

bowtie2 -p 12  -x indexed-genome -U $2 -S aligned-reads.sam





# Filtering the data and keeping only unmapped reads.

echo -e '\n Filtering out mapped reads... \n'

samtools view -f 0x4 -@ 12 aligned-reads.sam > unmapped-reads.bam

echo -e '\n converting unmapped-reads.bam to fasta format... \n'

samtools fasta unmapped-reads.bam > unmapped-reads.fasta


# Assembling the contigs from the unmapped reads.

#echo -e '\n Creating contigs with RepARK... \n'

#./RepARK-master/RepARK.pl -p 12 -l unmapped-reads.fasta  # results in repeat_lib.fasta

echo -e '\n Creating contigs with minia... \n'

minia -in unmapped-reads.fasta -nb-cores 12  # results in contig.fa



echo -e '\n RepARK alignment results in repeat_lib.fasta \n'

echo -e '\n Minia alignment results in contig.fasta \n'