Hi there,
I’m analyzing illumina data, and my summary after alignment produces a minimum start and end of both -1. I can’t seem to find anything on the forum regarding this… I know this is probably resulting from my screening parameters, and also leading to only unique taxonomy levels of taxonomy further down the pipeline… What’s causing this? What can I do to change this?
That’s generally a sign that the alignment didn’t work, perhaps because the reads were in the wrong orientation. If you post all of your commands we can help you figure this out.
What percentage of your reads have start and end values of -1? Non-specific amplicons will do this when you align them and we generally just chuck them when we run screen.seqs in the next step and move on…
I did remove them with screen.seqs, but when I moved on to filter.seqs, it gave an error ([ERROR]: Sequences are not all the same length, please correct)
and then with pre.cluster ([ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned.), so I fear that something went awry with my alignment.