I generated 40000000 paired-end reads by using flux simulator, and I found many of the reads are truncated.

I set the length of reads 100 bases, and many of the generated reads are only less than 10 bases long. Is it normal? Why?


Thank you.




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  1. Sorry for the delay in responding, it was a difficult week. If reads are truncated,it means that the fragment that was sequenced was shorter than the read length.

    Depending on the fragmentation method and parameters, short fragments can occur. If you use size filtering (FILTERING YES), then you can control that the size of the fragments matches the length of the reads you plan to sequence. To minimize the amount of fragments that are lost by size selection, fragmentation parameters should be set to maximize reads in the range of selected sizes.