# 454SOP

**URL:** https://forum.mothur.org/t/454sop/2728
**Category:** Commands in mothur
**Created:** [February 24, 2016, 1:57pm UTC](https://forum.mothur.org/t/454sop/2728 "2016-02-24T13:57:30Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![mashhood](https://avatars.discourse-cdn.com/v4/letter/m/f9ae1b/32.png) [@mashhood](https://forum.mothur.org/u/mashhood)
#### Post date: [February 24, 2016, 1:57pm UTC](https://forum.mothur.org/t/454sop/2728/1 "2016-02-24T13:57:30Z")

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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

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<div class="post-metadata">

### Author: ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [February 25, 2016, 12:50pm UTC](https://forum.mothur.org/t/454sop/2728/2 "2016-02-25T12:50:05Z")

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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

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<div class="post-metadata">

### Author: ![mashhood](https://avatars.discourse-cdn.com/v4/letter/m/f9ae1b/32.png) [@mashhood](https://forum.mothur.org/u/mashhood)
#### Post date: [February 29, 2016, 10:02am UTC](https://forum.mothur.org/t/454sop/2728/3 "2016-02-29T10:02:36Z")

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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

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<div class="post-metadata">

### Author: ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)
#### Post date: [March 7, 2016, 12:51pm UTC](https://forum.mothur.org/t/454sop/2728/4 "2016-03-07T12:51:08Z")

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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