I have a problem with finding the start and end position for screen.seqs after alignment (I’ve used the silva alignment database). I’m following the 454 SOP, and I’ve sequenced the V6-V9 region. I went through the Sogin example and noticed that they skipped the screen.seqs step and immediately run the filter.seqs command. Will this also be better for my dataset?
You don’t really want to follow the Sogin example, that’s very dated at this point. Do you know which direction the sequencing was done from? Did they start at V9 and work back to V6 or V6 towards V9? I suspect you want to set end to equal something like 37000 and then optimize for the start position. Regardless, it is a bit weird that they don’t all start (or end) at a similar coordinate. Do you have more details on what was done?
Thank you for your reply. Sequencing was done from V6 to V9. I think I made a mistake with my oligos file so the trim.seqs and downstream commands gave the weird results. I ran everything again this morning, and summary.seqs after alignment (with the silva database and flip=T) looks much better. Can I use 31189 as the start position and optimize the end?