I'm aligning some mouse RNA-Seq data (paired, 2x101) against the genome using STAR. After that, I analysed the insert size with Picard. Here are the two kinds of Insert Size Histograms. Which the first one seems so weird, can anyone explain to me what reasons can lead to the first Histogram?
(The data with the first Histogram has low alignment rate, after some changes of parameters , the alignment rate is better but it has high percentage of reads mapped to multiple loci. I am looking for the reasons...)
Thanks a lot!