screening fasta files and not group files?

Dear all,
I am revising the mothur pipeline I used for my 16S rRNA pyrosequencing data and I have the following doubt: I decided to remove from my dataset those sequences with length less than 250 bp in order to improve taxonomic classification. To do so, I used the following command:

screen.seqs(fasta=crdd1.shhh.trim.unique.good.filter.unique.precluster.pick.pick.fasta, minlength=250).

I noticed thought that by using the command above I removed sequences only from the fasta file and not from the group file. I believe this may be tricky for downstream analyses. For example, when I wanted to normalize the number of sequences in each of my samples, I noticed that in the group file I still have all my sequences. In other words, I did not remove sequences shorter than 250 bp from my group file only from my fasta file. Therefore, would I be normalizing my data for a number greater that the one it should be?

Would any of you out there have any comment or suggestion on how to solve that?


When you run the screen.seqs() command, add your group file as a parameter. That will keep them both consistent for other commands.

You also will want to add your names file to screen.seqs.