Hello!
We use PGM for target sequencing. Picture of alignment for single amplicon is shown in attachment. Can someone explain why some reads are trimmed in the 3' end (i.e. reads dont form straight stack in the picture)? I mean at what stage of sequencing it happends. And can be 5' end trimmed? Trimming after sequencing by phred quatility was not done. 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!
We use PGM for target sequencing. Picture of alignment for single amplicon is shown in attachment. Can someone explain why some reads are trimmed in the 3' end (i.e. reads dont form straight stack in the picture)? I mean at what stage of sequencing it happends. And can be 5' end trimmed? Trimming after sequencing by phred quatility was not done. 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!
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