Hey,
This is not really a bug, more just a question. I amplified 927f-1392r so am roughly expecting 400bp sequences once the primers have been removed, but as soon as I come out of shh.flows I have around 270 bp sequences. I was just wondering if anyone has an idea of why that could be?
Colin
Hi Colin,
If you’re following the SOP, then in trim.flows we trim all flowgrams to 450 flows - this works out to be ~270-300 bp. By the time you remove the barcodes / primers it drops to about 250-270 bp. The problem is that the data quality on all sequencing platforms degrades with length and as we showed in our 2012 PLoS ONE paper we get the best error redcution by limiting the number of flows to 450.
Pat
Thank you…