Hi, I had a detailed view on the insert size distribution of NGS read pairs from a BAM file using SAMtools stats of samtools 1.8 with htslib 1.8. The BAM file with the mapped reads represents a library where transposon-based fragmentation resulted in fragments that partly were shorter than the read lengths of the subsequent sequencing run on an Illumina instrument. Surprisingly, as you may see from the included diagram, the number of read pairs increased by almost exactly 100% when the insert size exceeded 150, which was the number of cycles in the sequencing run. This phenomenon was not obvious from experimental measurements of the library fragment lengths.
What might cause this phenomenon, and is there a way to avoid it in case I made a mistake? The alignment was generated using bwa bwasw and subsequently processed using samtools fixmate and samtools sort. I were glad to understand this puzzling effect. Frank Dr. rer. nat. Frank Vorhölter Molekularbiologe Überörtliche Berufsausübungsgemeinschaft Medizinisches Versorgungszentrum Dr. Eberhard & Partner Dortmund MVZ-Haus 1: Brauhausstr. 4 44137 Dortmund, Germany Tel.: +49 231 9572 6612
1181240333-L_insert-size.csv;filename*0*=iso-8859-1''%31%31%38%31%32%34%30%33%33%33%2D%4C%5F%69%6E%73%65
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