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anno_human.sh
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anno_human.sh
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#!/bin/bash
#a demo for generate splicing events and sequence features
###############################################################
# #
# Define splicing events and fetch features for human #
# #
###############################################################
# directory for your data and briekit executable files
DATA_DIR=~/research/annotation/human
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_human/release_25/GRCh38.p7.genome.fa.gz -O $DATA_DIR/GRCh38.p7.genome.fa.gz
wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz -O $DATA_DIR/gencode.v25.annotation.gtf.gz
wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/phastCons100way/hg38.phastCons100way.bw -O $DATA_DIR/hg38.phastCons100way.bw
gzip -d $DATA_DIR/*fa.gz
chmod +x $DATA_DIR/bigWigSummary
anno_ref=$DATA_DIR/gencode.v25.annotation.gtf.gz
fasta=$DATA_DIR/GRCh38.p7.genome.fa
### 2. Generate splicing events
$BIN_DIR/briekit-event -a $anno_ref -o $DATA_DIR/human_AS
### 3. Splicing events filtering
$BIN_DIR/briekit-event-filter -a $DATA_DIR/human_AS/SE.gff3.gz --anno_ref $anno_ref -r $fasta
$BIN_DIR/briekit-event-filter -a $DATA_DIR/human_AS/SE.gff3.gz --anno_ref $anno_ref -r $fasta \
-o $DATA_DIR/human_AS/SE.lenient.gtf --add_chrom chrX,chrY --as_exon_min 10 --as_exon_max 100000000 \
--as_exon_tss 10 --as_exon_tts 10 --no_splice_site #--keep_overlap
### 4. Extacting sequence feature for BRIE
phast=$DATA_DIR/hg38.phastCons100way.bw
bigWigSummary=$DATA_DIR/bigWigSummary
feature=$DATA_DIR/human_AS/human_factors.SE.filtered.csv.gz
$BIN_DIR/briekit-factor -a $DATA_DIR/human_AS/SE.filtered.gff3.gz -r $fasta -c $phast -o $feature -p 20 --bigWigSummary $bigWigSummary
feature=$DATA_DIR/human_AS/human_factors.SE.lenient.csv.gz
$BIN_DIR/briekit-factor -a $DATA_DIR/human_AS/SE.lenient.gff3.gz -r $fasta -c $phast -o $feature -p 20 --bigWigSummary $bigWigSummary