BAM reads much longer than fastq?
I have some paired-end RNAseq data that I downloaded (so, not mine). I started with their fastq files and have run them through Trimmomatic and STAR Aligner. I am currently trying to call peaks via MACS2, but got an error when I told MACS2 a too small fragment size. MACS2 is saying the fragment sizes in my BAM files are ~1700bp.
The paper these data came from said they used read lengths of 100bp and this was confirmed when I ran FASTQC on their fastq files.
What could have happened along the way?
1 answer
See this thread for an explanation of how these terms are related: What is the difference between a Read and a Fragment in RNA-seq?
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