Question

BAM reads much longer than fastq?

0

Entering edit mode

2.1 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 • 616 views

ADD COMMENT • link updated 2.1 years ago by GenoMax 141k • written 2.1 years ago by Jay • 0

score 1 · Answer 1 · 2022-03-25

1

Entering edit mode

2.1 years ago

GenoMax 141k

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 2.1 years ago by GenoMax 141k

0

Entering edit mode

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

ADD REPLY • link 2.1 years ago by Jay • 0

1

Entering edit mode

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