1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
|
#!/bin/sh -e
VCF=./example/genotypes.vcf
DIR_OUT=./OptimiR_Results_Dir
# MATURES=./optimir/resources/fasta/hsa_matures_miRBase_v21.fa
# HAIRPINS=./optimir/resources/fasta/hsa_hairpins_miRBase_v21.fa
# GFF3=./optimir/resources/coordinates/hsa_miRBase_v21.gff3
# First prepare library if OptimiR is launched in parallel jobs locally - or better, on a cluster. (In this example, they are launched sequentially)
optimir libprep \
-v $VCF \
-o $DIR_OUT # \
# -m $MATURES \
# -p $HAIRPINS \
# -g $GFF3
# Launch OptimiR on each sample (parallel computation is recommanded for many samples)
optimir process \
--fq ./example/S1.fq.gz \
--vcf $VCF \
--gff_out \
--dirOutput $DIR_OUT
optimir process \
--fq ./example/S2.fq.gz \
--vcf $VCF \
--gff_out \
--dirOutput $DIR_OUT
# Make summary files
optimir summarize --dir $DIR_OUT/OptimiR_Results
|
