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