Help for Processing improved sequences in align.seqs

Commands in mothur
1

Hi,

I am new to DNA Sequencing. I was using SOP of mothur Miseq.
i used these steps,

mothur > align.seqs(fasta=stability.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)

mothur > summary.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table

Start End NBases Ambigs Polymer NumSeqs
Minimum: -1 -1 0 0 1 1
2.5%-tile: 1 3 2 0 1 18427
25%-tile: 1 3 2 0 1 184265
Median: 1 3 2 0 1 368530
75%-tile: 1 3 2 0 1 552795
97.5%-tile: 13422 13425 16 0 3 718633
Maximum: 13425 13425 108 0 11 737059
Mean: 1197.86 1278.85 2.97542 0 1.16595

of unique seqs: 664782

total # of seqs: 737059

I wanted to know why the Minimum value starts from -1? i thought it may be the mismatch of sequences.

While Screening i gave,
screen.seqs(fasta=stability.trim.contigs.good.unique.align, count=stability.trim.contigs.good.count_table, summary=stability.trim.contigs.good.unique.summary, start=1, end=13425, maxhomop=8),

The stability.trim.contigs.good.unique.good.align is blank.

Kindly help me what is the error.

Thanks,
Ramya.

2

http://www.mothur.org/wiki/Screen.seqs Setting the end parameter removes any sequence that ends before that value. So end=13425 will remove most of your sequences. The start value is removing the rest because it will remove any sequences that don’t start by 1.

3

Hi,

Thanks for your reply.


Start End NBases Ambigs Polymer NumSeqs Minimum: -1 -1 0 0 1 1 2.5%-tile: 1 3 2 0 1 18427 25%-tile: 1 3 2 0 1 184265 Median: 1 3 2 0 1 368530 75%-tile: 1 3 2 0 1 552795 97.5%-tile: 13422 13425 16 0 3 718633 Maximum: 13425 13425 108 0 11 737059 Mean: 1197.86 1278.85 2.97542 0 1.16595 # of unique seqs: 664782 total # of seqs: 737059

May i know what is mean by -1 in the minimum.

Thanks,
Ramya.

4

-1 is the default location mothur starts with. When you see -1 in a summary value, it usually indicates all the sequence’s bases were removed so mothur can’t find a start position or end position. The alignment looks like it removed most of your bases in the sequences. Are you sure you are using the correct template?

5

Hi,

Thank you!
The data is with V8 region, so the database should be whole silva, but i took only bacteria so the alignment is less.

Regards,
Ramya.