Quality trimming

Source the configuration file:

source conf_cluster.conf

Use Sickle to filter out low quality reads. First create the directory for storing quality-filtered reads:

mkdir -p $wd/$PRJ_NAME/1_FilteredReads

See the number of raw reads:

for i in $SAMPLE_LIST; do
        echo "Sample $i"
        echo "Reads $i"
        grep "@" $INPUT_DIR/$i.R1.fastq | wc -l
done

Have a look to Sickle help:

sickle pe --help

Now run Sickle on your data:

for i in $SAMPLE_LIST; do
        sickle pe \
        -f $INPUT_DIR/$i.R1.fastq \
        -r $INPUT_DIR/$i.R2.fastq \
        -t sanger \
        -o $FILT_READS/filtered.$i.R1.fastq \
        -p $FILT_READS/filtered.$i.R2.fastq \
        -s $FILT_READS/filtered.single.$i.fastq \
        -q $AV_READS_Q \
        -l $AV_READS_L
done

See the number of filtered reads:

for i in $SAMPLE_LIST; do
        echo "Sample $i"
        echo "Filtered reads $i"
        grep "@" $FILT_READS/filtered.$i.R1.fastq | wc -l
done