Ion torrent errors in fastq

Question

[anasofiamoreira94]

In my lab we use S5 from ion torrent. So we extract the fastq files from S5 and we analyze the data. We start by trimming the fastq files, removing low quality reads, small size. However, this sequences produces a lot of insertions in the middle of the fastqs and when we perform an alignment the %ID is really low... Can someone tell me how to pass this problem? Thanks!

[Friederike]

can you describe a bit more what you mean by "insertions in the middle of fastqs"? What does the FastQC result look like for the trimmed files?