This might be a bug, or me not understanding exactly how to set the commands… But I am very confused.
I am using
Last updated: 11/14/2019
In CentOS Linux 7 (Core)
In the step with deblur, there is a mistach in the the number of reads at the beginning and at the end. I tried both:
pre.cluster(fasta=current, name=current, diffs=1, method=deblur)
pre.cluster(fasta=current, count=current, diffs=1, method=deblur) after making a count table.
The fasta points to the last unique fasta file, and the name is the last namefile (obviously)
As a result, there are 50% of the reads missing after this step in the count.table created by this step. It uses the alignment from the unique file, but apparently it does not carry forward the counts from the namefile or the count.table. The new count of reads is larger than the previous number of uniques (so, it is reading the original count table) but, half of the reads (in number) of the total number of reds are missing.