I have a PE 100 reads from hiseq 2000, 100PE reads =166,867,542 PE reads. when i opened it by fastqc, it only shows total sequence:16000000. Anyway, I just wanted to eliminate adapter sequences by Trimmomatic, so I use:
java -classpath ~/Software/Trimmomatic-0.17/trimmomatic-0.17.jar org.usadellab.trimmomatic.TrimmomaticPE -phred33 1145LJZ0007_read1.txt 1145LJZ0007_read2.txt reads_fwd_paired.fq.gz reads_fwd_UNpaired.fq.gz reads_rev_paired.fq.gz reads_rev_UNpaired.fq.gz ILLUMINACLIP:illuminaContaminants.fa:2:40:15
I ended up with 15845809. I checked reads_fwd_paired.fq.gz, the last line is HWI-ST829:1260CWTABXX:5:1104:6650:64208 1:N:0:..., which means the last read from tile 1104. This means you just had 4 tiles processed. Usually there are 48 tiles per lane. Therefore only 10% reads got processed. I wonder if Trimmomatic has 16000000 read limit, which CASAVA has it for ELAND. If that is the case, where does this read limit comes from and how to bypass this problem. Thanks.
java -classpath ~/Software/Trimmomatic-0.17/trimmomatic-0.17.jar org.usadellab.trimmomatic.TrimmomaticPE -phred33 1145LJZ0007_read1.txt 1145LJZ0007_read2.txt reads_fwd_paired.fq.gz reads_fwd_UNpaired.fq.gz reads_rev_paired.fq.gz reads_rev_UNpaired.fq.gz ILLUMINACLIP:illuminaContaminants.fa:2:40:15
I ended up with 15845809. I checked reads_fwd_paired.fq.gz, the last line is HWI-ST829:1260CWTABXX:5:1104:6650:64208 1:N:0:..., which means the last read from tile 1104. This means you just had 4 tiles processed. Usually there are 48 tiles per lane. Therefore only 10% reads got processed. I wonder if Trimmomatic has 16000000 read limit, which CASAVA has it for ELAND. If that is the case, where does this read limit comes from and how to bypass this problem. Thanks.
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