why bowtie2 doesn’t report longer than 500bp inserts?
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?
1 answer
By default, bowtie2 expects a maximum fragment length of 500 bp for paired-end alignments. To adjust this, change the -X or --maxins parameter.
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