-
Notifications
You must be signed in to change notification settings - Fork 0
/
FASTQC_runfile_081123_all_biofilm_081423.sh
82 lines (63 loc) · 4.24 KB
/
FASTQC_runfile_081123_all_biofilm_081423.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
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
#!/bin/bash
#MUST DO BEFORE:
#conda create -n multiqc_env -c bioconda -c conda-forge fastqc multiqc cutadapt
#conda activate multiqc
#export LC_ALL=en_US.UTF-8
#export LANG=en_US.UTF-8
project_shortname="all_biofilm_demux_081123"
workingPATH="/home/genomics/raw/all_biofilm_demux_081123" # Path to the parent directory. It is not the directory where are stored the fastqs. Should NOT finish with "/"
fastq_directory=$workingPATH/"FASTQ_files/cutadapt_trimmed" # Name of the folder containing the fastqs. It must be located in the parent directory.
scriptsPATH=$workingPATH/"FASTQC_MULTIQC_scripts_2023"
#cutadapt--------
#cd $fastq_directory
#for f in *R1_001.fastq.gz; do
# n=`echo $f | rev | cut -d _ -f 3- | rev` &&
# cutadapt -j 8 -g GTGYCAGCMGCCGCGGTAA -G CCGYCAATTYMTTTRAGTTT -o $n'_R1_001_trimmed.fastq.gz' -p $n'_R2_001_trimmed.fastq.gz' $f $n'_R2_001.fastq.gz'
#done
#read 1 fastqc, multiqc-------------------
cd $fastq_directory
#mkdir fastqc-R1
#fastqc *_R1_001_trimmed.fastq.gz -o fastqc-R1
cd fastqc-R1
#multiqc --export .
FASTQC_VAR1_80=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R1/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.80)
FASTQC_VAR1_85=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R1/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.85)
FASTQC_VAR1_90=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R1/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.9)
FASTQC_VAR1_95=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R1/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.95)
#read 2 fastqc, multiqc-------------------
cd ..
#mkdir fastqc-R2
#fastqc *_R2_001_trimmed.fastq.gz -o fastqc-R2
cd fastqc-R2
#multiqc --export .
FASTQC_VAR2_80=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R2/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.80)
FASTQC_VAR2_85=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R2/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.85)
FASTQC_VAR2_90=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R2/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.9)
FASTQC_VAR2_95=$($scriptsPATH/fastqc_per_base_sequence_quality_dropoff.py --input $fastq_directory/"fastqc-R2/multiqc_data/mqc_fastqc_per_base_sequence_quality_plot_1.txt" --cutoff 0.95)
#run dada2 filterandtrim-------------------
cd $scriptsPATH
Rscript --vanilla dada2_runfile.r ${fastq_directory} ${FASTQC_VAR1_80} ${FASTQC_VAR2_80}
DADA2_VAR_80=$(sed '2q;d' $fastq_directory/average_quality.txt)
rm $fastq_directory/filtered/*_filt.fastq.gz
rmdir $fastq_directory/filtered
Rscript --vanilla dada2_runfile.r ${fastq_directory} ${FASTQC_VAR1_85} ${FASTQC_VAR2_85}
DADA2_VAR_85=$(sed '2q;d' $fastq_directory/average_quality.txt)
rm $fastq_directory/filtered/*_filt.fastq.gz
rmdir $fastq_directory/filtered
Rscript --vanilla dada2_runfile.r ${fastq_directory} ${FASTQC_VAR1_90} ${FASTQC_VAR2_90}
DADA2_VAR_90=$(sed '2q;d' $fastq_directory/average_quality.txt)
rm $fastq_directory/filtered/*_filt.fastq.gz
rmdir $fastq_directory/filtered
Rscript --vanilla dada2_runfile.r ${fastq_directory} ${FASTQC_VAR1_95} ${FASTQC_VAR2_95}
DADA2_VAR_95=$(sed '2q;d' $fastq_directory/average_quality.txt)
rm $fastq_directory/filtered/*_filt.fastq.gz
rmdir $fastq_directory/filtered
#print values from multiqc-------------------
printf "\n"
paste <(echo "cut-off") <(echo "") <(echo "read1") <(echo "read2") <(echo "perc. retain")
paste <(echo "") <(echo "80%") <(printf %s "$FASTQC_VAR1_80") <(printf %s "$FASTQC_VAR2_80") <(printf %s "$DADA2_VAR_80")
paste <(echo "") <(echo "85%") <(printf %s "$FASTQC_VAR1_85") <(printf %s "$FASTQC_VAR2_85") <(printf %s "$DADA2_VAR_85")
paste <(echo "") <(echo "90%") <(printf %s "$FASTQC_VAR1_90") <(printf %s "$FASTQC_VAR2_90") <(printf %s "$DADA2_VAR_90")
paste <(echo "") <(echo "95%") <(printf %s "$FASTQC_VAR1_95") <(printf %s "$FASTQC_VAR2_95") <(printf %s "$DADA2_VAR_95")
printf "\n"
exit 0