Hello, I’m currently facing an issue where I placed sub.sample after remove.lineage. After running sub.sample(
fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta,
count=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table,
size=16794
),
the result obtained is a random draw of 16,794 sequences from the total pool,whereas I intended to draw 16,794 sequences from each sample. Why is this happening? What should I do next to achieve the desired outcome?
My suspicion is that you only have one group represented in stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.count_table. Can you run count.groups on the file and see what you get? You probably left out the group information at some step in your pipeline. I’d suggest running count.groups after each step to see where the grouping information was removed. That will tell you where you have a problem. You might try it right after make.contigs to insure you had them from the beginning
Pat
However, after remove.lineage, I ran count.groups, which displayed the number of sequences for each group and the minimum number of sequences among the samples. I believe the grouping information was preserved. If I want to perform sub.sample after remove.lineage, is it feasible? Could you provide me with the code for that?
Can you try running sub.sample with persample=true as one of the arguments? You can learn more about the argument here: sub.sample
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