I used The 9th column of `.bam` file to get the insert size of atac-seq data.

```
samtools view bam/${FILE}"_mm10.bam" | awk '$9>0' | cut -f 9 | sort | uniq -c | sort -b -k2,2n > insert_size_plotting/${FILE}".txt"
```

But I found all of the inserts are less than 500bp, 
From the insert size plot, I can see there should be longer than 500bp inserts, but why bowtie2 doesn’t report >500bp inserts?
![enter image description here][1]
Thanks


  [1]: /media/images/c6891381-0797-4efd-8f9f-5d375f85
By default, bowtie2 expects a maximum fragment length of 500 bp for paired-end alignments. To adjust this, change the `-X` or `--maxins` parameter. 

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml