why bowtie2 doesn’t report longer than 500bp inserts?

Question

[Dan]

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? Thanks

Answer 1

[acvill]

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

[Dan]

I am wondering can I recalculate the insert size from .bam files? Thanks a lot

[acvill]

How To Get The "Library Insert Size" Out Of A Sam/Bam File?
Estimate Insert Size In Paired-End/Mate-Pair