text: user9508: I have a paired-end data. It is from small part of human genome not a WGS or WES. I use BWA for alignment and do variant calling. Since I had some false positives I wanted to do trimming.
  I used trimmomatic with command:
  trimmomatic PE -phred33 -threads 2 read1.fastq.gz read2.fastq.gz read1_trimmed.fastq read2_trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15`
  
  I do not know why but I have this output:
  Input Read Pairs: 1834513 
  Both Surviving: 1822034 (99.32%) 
  Forward Only Surviving: 5740 (0.31%)
  Reverse Only Surviving: 417 (0.02%)
  Dropped: 6322 (0.34%)
  TrimmomaticPE: Completed successfully
  
  I do not have any adapters since the are removed in bcl2fastq step. In FASTQ quality control I have seen that quality of reverse and forward reads are similar in quality but trimmomatic trimmed many reads in reverse file. I cannot do alignment with these files, BWA gives a warning that says:
  [bseq_read] the 2nd file has fewer sequences. 
  [process] read 155012 sequences (16693324 bp)... 
  [bseq_read] the 2nd file has fewer sequences.
  
  Is there anyone who faced a problem like this before?
  Thank you in advance
  
  user4282: Maybe you need to remove the unpaired reads:
  trimmomatic PE -phred33 -threads 2 \
      read1.fastq.gz read2.fastq.gz \
      read1_trimmed.fastq.gz read1_unique.fastq.gz \
      read2_trimmed.fastq.gz read2_unique.fastq.gz \
      LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15
  
  Then you can try with bwa.
  
original_text: 9508: <p>I have a paired-end data. It is from small part of human genome not a WGS or WES. I use BWA for alignment and do variant calling. Since I had some false positives I wanted to do trimming.</p>
  <p>I used trimmomatic with command:</p>
  <pre><code>trimmomatic PE -phred33 -threads 2 read1.fastq.gz read2.fastq.gz read1_trimmed.fastq read2_trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15`
  </code></pre>
  <p>I do not know why but I have this output:</p>
  <pre><code>Input Read Pairs: 1834513 
  Both Surviving: 1822034 (99.32%) 
  Forward Only Surviving: 5740 (0.31%)
  Reverse Only Surviving: 417 (0.02%)
  Dropped: 6322 (0.34%)
  TrimmomaticPE: Completed successfully
  </code></pre>
  <p>I do not have any adapters since the are removed in <code>bcl2fastq</code> step. In FASTQ quality control I have seen that quality of reverse and forward reads are similar in quality but trimmomatic trimmed many reads in reverse file. I cannot do alignment with these files, BWA gives a warning that says:</p>
  <pre><code>[bseq_read] the 2nd file has fewer sequences. 
  [process] read 155012 sequences (16693324 bp)... 
  [bseq_read] the 2nd file has fewer sequences.
  </code></pre>
  <p>Is there anyone who faced a problem like this before?</p>
  <p>Thank you in advance</p>
   4282: <p>Maybe you need to remove the unpaired reads:</p>
  <pre><code>trimmomatic PE -phred33 -threads 2 \
      read1.fastq.gz read2.fastq.gz \
      read1_trimmed.fastq.gz read1_unique.fastq.gz \
      read2_trimmed.fastq.gz read2_unique.fastq.gz \
      LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15
  </code></pre>
  <p>Then you can try with bwa.</p>
  