How to know if bowtie2 -X fragment length (default : 500bp) is suitable for alignment of my data?

The project that I am doing now requires me to filter of hg19 sequences from my data set. I have trimmed my read lengths to 50 bp with Qphred = 20. Next, I will be using bowtie2 to align the...

02 October 2017 7,349 4 View