What Maxlength and maxhomop should i use?

I have run the following command
make.contigs(file=stability.files, processors=16)
and generated a summary table using the following command
summary.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table).
Summany table given below in the picture.

Now I wish to run any one from among the following commands(to remove ambiguous base calls):
make.contigs(file=stability.files, maxambig=, maxlength=, maxhomop=)
screen.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table, maxambig=, maxlength=, maxhomop=)
I don’t know how to choose the values for the following parameters
maxambig=, maxlength=, maxhomop=
Can some one hep me with this and please explain how to choose these parameters?


maxambig is always = to zero, maxlength should be the length of the amplicon you are sequencing and maxhomop, well just use what is in the SOP, it should do the trick.

Best of success

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Thank you very much for replying.

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