-
Notifications
You must be signed in to change notification settings - Fork 2
/
anno_mouse.sh
48 lines (33 loc) · 2.14 KB
/
anno_mouse.sh
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
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
#!/bin/bash
#a demo for generate splicing events and sequence features
###############################################################
# #
# Define splicing events and fetch features for mouse #
# #
###############################################################
# directory for your data and briekit executable files
DATA_DIR=~/research/annotation/mouse
BIN_DIR=~/anaconda2/bin
### 1. download files
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary -O $DATA_DIR/bigWigSummary
wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/GRCm38.p5.genome.fa.gz -O $DATA_DIR/GRCm38.p5.genome.fa.gz
wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M12/gencode.vM12.annotation.gtf.gz -O $DATA_DIR/gencode.vM12.annotation.gtf.gz
wget ftp://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/mm10.60way.phastCons.bw -O $DATA_DIR/mm10.60way.phastCons.bw
gzip -d $DATA_DIR/GRCm38.p5.genome.fa.gz
chmod +x $DATA_DIR/bigWigSummary
anno_ref=$DATA_DIR/gencode.vM12.annotation.gtf.gz
fasta=$DATA_DIR/GRCm38.p5.genome.fa
### 2. Generate splicing events
$BIN_DIR/briekit-event -a $anno_ref -o $DATA_DIR/mouse_AS
### 3. Splicing events filtering
$BIN_DIR/briekit-event-filter -a $DATA_DIR/mouse_AS/SE.gff3.gz --anno_ref $anno_ref -r $fasta
$BIN_DIR/briekit-event-filter -a $DATA_DIR/mouse_AS/SE.gff3.gz --anno_ref $anno_ref -r $fasta \
-o $DATA_DIR/mouse_AS/SE.lenient.gtf --add_chrom chrX,chrY --as_exon_min 10 --as_exon_max 100000000 \
--as_exon_tss 10 --as_exon_tts 10 --no_splice_site #--keep_overlap
### 4. Extacting sequence feature for BRIE
phast=$DATA_DIR/mm10.60way.phastCons.bw
bigWigSummary=$DATA_DIR/bigWigSummary
feature=$DATA_DIR/mouse_AS/mouse_factors.SE.filtered.csv.gz
$BIN_DIR/briekit-factor -a $DATA_DIR/mouse_AS/SE.filtered.gff3.gz -r $fasta -c $phast -o $feature -p 20 --bigWigSummary $bigWigSummary
feature=$DATA_DIR/mouse_AS/mouse_factors.SE.lenient.csv.gz
$BIN_DIR/briekit-factor -a $DATA_DIR/mouse_AS/SE.lenient.gff3.gz -r $fasta -c $phast -o $feature -p 20 --bigWigSummary $bigWigSummary