Question: Paired-end insert size upper limit
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lukacdm • 0 wrote:
I am mapping paired-end reads using Bowtie2 and setting "maximum insert size for valid paired-end alignments" to 500 bases. However, when I calculate the insert sizes of the resulting bam files using Picard Insert Size Metrics I frequently see one or two inserts per file that exceed 20000 bases. Is the Bowtie2 mapping incorrectly returning very large inserts, or is the Picard software mis-analyzing the bam file? If these large inserts are really coming from incorrect mapping, how can I remove them from the bam files so my downstream analyses are not affected?
