Question

BAM reads much longer than fastq?

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2.8 years ago

Jay • 0

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?

ChIPseq read length • 785 views

ADD COMMENT • link updated 2.8 years ago by GenoMax 148k • written 2.8 years ago by Jay • 0

score 1 · Answer 1 · 2022-03-25

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2.8 years ago

GenoMax 148k

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?

ADD COMMENT • link 2.8 years ago by GenoMax 148k

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Ah, I was missing a piece of the puzzle. Thank you so much!

ADD REPLY • link 2.8 years ago by Jay • 0

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You have tagged this RNAseq but then are asking about MACS2. I assume that is a typo? MACS2 is for ChIPseq analysis.