Tweet
Hi
when I run bwa-mem with the options "-w 100 -O 5 -E 0.4" on paired end data I get the distribution of deletion sizes as shown in the attached image.
Can anybody give a hint where this spiky pattern comes from? It is not observed when aligning with bwa-aln or bowtie2, so it does not seem to be due to the sample. Any hint would be welcome.
best regards
hubert
when I run bwa-mem with the options "-w 100 -O 5 -E 0.4" on paired end data I get the distribution of deletion sizes as shown in the attached image.
Can anybody give a hint where this spiky pattern comes from? It is not observed when aligning with bwa-aln or bowtie2, so it does not seem to be due to the sample. Any hint would be welcome.
best regards
hubert