454SOP

Commands in mothur
1

Dear Schloss,
Thanks for all the help which you provided me when I was working on MiSeqSOP and further in my analysis… I have now started to work om 454SOP. Initial steps are compleatly different from MiSeq mothur analysis.
I stuck up in the starting itself, I find 11 flow files but it is mentioned 21 flow files should be there.
It is mentioned that you will not provide sff file then I am not able to understand how the command

mothur > sffinfo(sff=GQY1XT001.sff, flow=T) will work.

The data which you provided contains flow, fasta,qual,count and group files. I am not able to understand how to club all fasta file so to use command

mothur > summary.seqs(fasta=GQY1XT001.fasta)

Please help so that I can start 454SOP.

Thanks

2

What I have given is a subset of the overall dataset. There is a second link next to the link you clicked to get the full dataset.

Pat

3

Thanks for your help. Full dataset is in binary file and I am not able to operate that… The result which we are getting in 454SOP is for full dataset or subset…Because when I am merging all the Fasta file to create GQY1XT001.fasta I am getting very less number of seqence… For merging Fasta file I use this command from ur subset. Am i correct???

mothur > merge.files(input=GQY1XT001.F003D000.shhh.fasta-GQY1XT001.F003D002.shhh.fasta-GQY1XT001.F003D004.shhh.fasta-GQY1XT001.F003D006.shhh.fasta-GQY1XT001.F003D008.shhh.fasta-GQY1XT001.F003D142.shhh.fasta-GQY1XT001.F003D144.shhh.fasta-GQY1XT001.F003D146.shhh.fasta-GQY1XT001.F003D148.shhh.fasta-GQY1XT001.F003D150.shhh.fasta-GQY1XT001.MOCK.GQY1XT001.shhh.fasta, output=GQY1XT001.fasta, outputdir=ITS)

mothur > summary.seqs(fasta=ITS/GQY1XT001.fasta)

Using 1 processors.

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 273 273 0 3 1
2.5%-tile: 1 281 281 0 4 548
25%-tile: 1 289 289 0 4 5472
Median: 1 296 296 0 4 10944
75%-tile: 1 303 303 0 5 16415
97.5%-tile: 1 321 321 0 6 21339
Maximum: 1 338 338 0 8 21886
Mean: 1 297.363 297.363 0 4.45554

of Seqs: 21886

Output File Names:
ITS/GQY1XT001.summary

4

You would have to generate the original oligos file for the dataset to get all of the data. I suspect what you have is sufficient to do the tutorial from the beginning.

Pat