What criteria to remove shorter and longer of contigs sequence using screen.seqs

Theory behind mothur
1

Hi, What length i should choose for screen.seqs command from my contigs in below summary . We used V4 region of 18S, using general eukaryotic primers. I am not getting about length to select usually for 16s RNA it ~250bp but here contigs showing length 348bp to 602bp. Thanks

mothur > summary.seqs(fasta=stability.trim.contigs.fasta)

Using 4 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 35 35 0 2 1
2.5%-tile: 1 348 348 0 4 7630
25%-tile: 1 418 418 0 5 76297
Median: 1 421 421 2 6 152593
75%-tile: 1 427 427 9 6 228889
97.5%-tile:1 567 567 29 7 297556
Maximum: 1 602 602 118 300 305185
Mean: 1 427.682 427.682 6.03693 5.69793

2

what were your primers?

3

The V4 region of 18S, using general eukaryotic primers
TAReuk454FWD1 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCAGCASCYGCGGTAATTCC-3’)and
TAReukREV3 (5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACTTTCGTTCTTGATYRA-3’).

4

How big was the amplicon that you sequenced? I don’t know those primers off the top of my head. you can do in silico pcr here. https://www.arb-silva.de/search/testprime/

5

Here are the primers…

forward CCAGCAGCGGTAATTCC
reverse ACTTTCGTTCTTGATA