Mean fragment size is short than read length

[xie186]

Command line:

callpeak -f BAMPE -g mm -t IP.bam -c input.bam -n test--outdir macs2_outdir/

Version: 2.1.2

Read length is 150 bps. But the "#1 mean fragment size " is 94 bps by macs2

#1 mean fragment size is determined as 94 bp from treatment

Could someone help me explain this? Thanks.

[wwang-chcn]

That means the major part of fragment size in you sequencing library is short than 150bp. If you run fastqc for you reads, you will probably find a increase of adapter content on the 3'.

[xie186]

Thanks for the reply @wwang-chcn.
This is the fastqc results:

It seems that there is no adapter contamination. I also checked the bam files generated. The reads were well aligned with "150M".