How to decide start end for screen.seqs

1

I am analysing 16S rRNA reads V4 region amplified using 515f and 806r primers. I used the coordinates for trimming the SILVA database as 11894 and 25319 (start and end). I am confused about what coordinates should I set for screen.seqs since I am going to run this script in the batch mode. here is the script I am using.

pcr.seqs(fasta=silva.nr_v132.bacteria.fasta, start=11894, end=25319, keepdots=F)
rename.file(input=silva.nr_v132.bacteria.pcr.fasta, new=silva.v4.fasta)
make.file(inputdir=., type=fastq, prefix=stability)
make.contigs(file=current, maxambig=0, maxlength=275, maxhomop=8)
unique.seqs(fasta=stability.trim.contigs.fasta, count=stability.contigs.count_table)
align.seqs(fasta=current, reference=silva.v4.fasta)
screen.seqs(fasta=current, count=current, start=1969, end=11551)

How do I decide the start and end corrdinates here? I know I need to use summary.seqs after align.sqs, but what if i am using this in batch mode? How do I tell the script to select the start and end coordinates?

summary.seqs(fasta=stability.trim.contigs.unique.align, count=stability.trim.contigs.count_table)
2

Hi Jaya -

Can you post the output that comes to the screen when you run summary.seqs?

Thanks,
Pat

3

I still have to run it on my actual sequences. But since I want to automate the process, this is what I have done for now, so that it can select the appropriate to use it as a general rule.

screen.seqs (fasta=current, count=current, summary=current, optimize=start-end, criteria=75)

Is it a nice strategy to use in general?

4

That may work. It would be better to see the output of summary.seqs. The start position value is the point at which sequences need to have started by and the end position is the point at which sequences should have ended by