Make.contigs doubt

Commands in mothur
1

As it was shown in Miseq SOP, the most occurring end length of the contig they have fixed the contig length, so in my data what length should I fix in screen.seqs? please do comment. We have sequenced v3-v4 region.
Our read length was 301*2 basepair.

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

Using 20 processors.

		Start	End	NBases	Ambigs	Polymer	NumSeqs
Minimum:	1	293	293	0	3	1
2.5%-tile:	1	443	443	0	4	118088
25%-tile:	1	448	448	0	5	1180879
Median: 	1	467	467	2	5	2361758
75%-tile:	1	472	472	8	6	3542637
97.5%-tile:	1	594	594	24	13	4605428
Maximum:	1	602	602	168	301	4723515
Mean:	1	469	469	5	5
# of unique seqs:	4723515
total # of seqs:	4723515

It took 396 secs to summarize 4723515 sequences.

Output File Names:
stability.trim.contigs.summary

Thanks
Priyanka

2

Sorry, but I do not understand your question.

Also, you’ll likely want to consult these blog posts…

Pat

3

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