PGM reads 3' end trimming

Question

[Max Ivon]

Hello!

We use PGM for target sequencing (signle end reading). Can someone explain why some reads are trimmed in the 3' end? I mean at what stage of sequencing it happends. And can be 5' end trimmed? There is no any strand bias of trimming. Reads are trimmed already in fastq file derived straightly from PGM, so it is not effect of any soft or tool.Trimming length differs from read to read, it is not constant.

Thanks in advance!

[Ashutosh Pandey]

What is your question? How you know that reads have been trimmed?