Hi everyone, I got really confused by some of the observations with my current data set (my second set of ChIP-Seq ever). After paired-end sequencing, I got 32 fastq.gz files for 16 samples. I use trimmomatic paired-end mode to trim illumina adaptors. Then, I ran BWA-MEM with the default parameters, using the paired reads from trimmomatic output. I then filtered for mapping quality > 5 and "IsProperPair" using Bamtools. Here's the problem: 5 out of 16 samples returned extremely small files. I ran Samtools "Stats" and found that while these files had lots of mapped reads, there were 0 proper pairs. I triple checked the input files and they were all matching paired reads.
Since my experience in ChIP-seq analysis is very limited, it'd be very helpful if someone can enlighten me on the cause of this problem and whether I can still use the alignment files without filtering for proper pairs. Thank you very much!