-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathtrim.sh
47 lines (39 loc) · 2.24 KB
/
trim.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
# Assumes Trimmomatic binaries in the $PATH
BASE=$1 # The argument to the script, use the name of the forward reads
ADAPTER="/home/stas/Documents/BIOINFO/Methanobacterium/GENOMES/adapters.fa"
# adapters.fa is a combination of Nextera seqs shipped with Trimmomatic 0.39
# and an overrepresented seq in the reads
THREADS=8
# Trim the reads
#java -jar /home/stas/Programs/Trimmomatic-0.39/trimmomatic-0.39.jar PE \
#-threads $THREADS -phred33 -basein $BASE -baseout $BASE-trimmed.fq.gz \
#ILLUMINACLIP:$ADAPTER:2:40:15:1:true \
#HEADCROP:10 \
#SLIDINGWINDOW:4:15 \
#MINLEN:230
#Input Read Pairs: 3320440 Both Surviving: 2124804 (63.99%) Forward Only Surviving: 87266 (2.63%) Reverse Only Surviving: 36128 (1.09%) Dropped: 1072242 (32.29%)
#java -jar /home/stas/Programs/Trimmomatic-0.39/trimmomatic-0.39.jar PE \
#-threads $THREADS -phred33 -basein $BASE -baseout $BASE-trimmed.fq.gz \
#ILLUMINACLIP:$ADAPTER:2:40:15:1:true \
#SLIDINGWINDOW:4:15 \
#MINLEN:230
#Input Read Pairs: 3320440 Both Surviving: 2239208 (67.44%) Forward Only Surviving: 78922 (2.38%) Reverse Only Surviving: 72348 (2.18%) Dropped: 929962 (28.01%)
#java -jar /home/stas/Programs/Trimmomatic-0.39/trimmomatic-0.39.jar PE \
#-threads $THREADS -phred33 -basein $BASE -baseout $BASE-trimmed.fq.gz \
#ILLUMINACLIP:$ADAPTER:2:40:15:1:true \
#HEADCROP:12 \
#SLIDINGWINDOW:4:15 \
#MINLEN:230
#Input Read Pairs: 3320440 Both Surviving: 2101285 (63.28%) Forward Only Surviving: 88991 (2.68%) Reverse Only Surviving: 30408 (0.92%) Dropped: 1099756 (33.12%)
#java -jar /home/stas/Programs/Trimmomatic-0.39/trimmomatic-0.39.jar PE \
#-threads $THREADS -phred33 -basein $BASE -baseout $BASE-trimmed.fq.gz \
#ILLUMINACLIP:$ADAPTER:2:40:15:1:true \
#SLIDINGWINDOW:4:15
#Input Read Pairs: 3320440 Both Surviving: 3318674 (99.95%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 1766 (0.05%) Dropped: 0 (0.00%)
java -jar /home/stas/Programs/Trimmomatic-0.39/trimmomatic-0.39.jar PE \
-threads $THREADS -phred33 -basein $BASE -baseout $BASE-trimmed.fq.gz \
ILLUMINACLIP:$ADAPTER:2:40:15:1:true \
SLIDINGWINDOW:4:15 \
MINLEN:240
#Input Read Pairs: 3320440 Both Surviving: 2124802 (63.99%) Forward Only Surviving: 87267 (2.63%) Reverse Only Surviving: 36129 (1.09%) Dropped: 1072242 (32.29%)