About the stability.files

[zzhubo]

I have confused how could I get the stablity.files of my data.I have try to run the test data and all is good. Whether should I type the file name of my data and save (But I have to much data more than thousands), or is there some command I missed ?
Thanks
Bo

[dwaite]

You generally need to make it yourself, since it’s the linker of your groups to file names. If you have a large number of samplesyou could use a bit of command line wizardry to simplify the process, for example I could generate the stability.files file presented in the MiSeq SOP using the following:

ls *R1_001.fastq | cut -f1 -d "_" > groupnames.txt
ls *R1_001.fastq > forward.txt
ls *R2_001.fastq > reverse.txt
paste groupnames.txt forward.txt > temp.txt
paste temp.txt reverse.txt > stability.files

Potentially you could try something similar, you just need to know whereabouts in the file name your sample information is, and what distinguishes forward/reverse reads.

[zzhubo]

@dwaite

You generally need to make it yourself, since it’s the linker of your groups to file names. If you have a large number of samplesyou could use a bit of command line wizardry to simplify the process, for example I could generate the stability.files file presented in the MiSeq SOP using the following:

ls *R1_001.fastq | cut -f1 -d "_" > groupnames.txt
ls *R1_001.fastq > forward.txt
ls *R2_001.fastq > reverse.txt
paste groupnames.txt forward.txt > temp.txt
paste temp.txt reverse.txt > stability.files

Potentially you could try something similar, you just need to know whereabouts in the file name your sample information is, and what distinguishes forward/reverse reads.

Really appreciate for your help.Although I still get my stability.files, but at least I have figure out I must get that by myself. Thank again!

[zzhubo]

@dwaite

You generally need to make it yourself, since it’s the linker of your groups to file names. If you have a large number of samplesyou could use a bit of command line wizardry to simplify the process, for example I could generate the stability.files file presented in the MiSeq SOP using the following:

ls *R1_001.fastq | cut -f1 -d "_" > groupnames.txt
ls *R1_001.fastq > forward.txt
ls *R2_001.fastq > reverse.txt
paste groupnames.txt forward.txt > temp.txt
paste temp.txt reverse.txt > stability.files

Potentially you could try something similar, you just need to know whereabouts in the file name your sample information is, and what distinguishes forward/reverse reads.

I have another question that you mentioned “command line wizardry” is a software or just type the commad in the mothur? Thank you!

[dwaite]

Ah, those commands I used (ls, cut, paste) are standard console commands on Linux and Mac computers. You can call them directly from the console, or from within mothur using the system() command. E.g.

mothur > system(ls *R1_001.fastq | cut -f1 -d "_" > groupnames.txt)
mothur > system(ls *R1_001.fastq > forward.tx)
...

[zzhubo]

@dwaite

Ah, those commands I used (ls, cut, paste) are standard console commands on Linux and Mac computers. You can call them directly from the console, or from within mothur using the system() command. E.g.

mothur > system(ls *R1_001.fastq | cut -f1 -d "_" > groupnames.txt)
mothur > system(ls *R1_001.fastq > forward.tx)
...

Really really appreciate your help! I will continue to learn how to use Mothur .