How to make a file that combine the three data files

Question

[flavobacteria]

it comes from the link for 16s rRNA analysis:

https://biomickwatson.wordpress.com/2014/04/21/a-mothur-tutorial-what-can-we-find-out-about-the-horse-gut-metagenome/

I was stuck here:

We start by creating a file which details how the fastq files relate to one another. We only have one group here, so this should be easy. I created horse.files such that it contains:

SRR952153       SRR952153_1.fastq       SRR952153_2.fastq

From there we can merge these using Mothur's make.contigs command:

mothur "#make.contigs(file=horse.files, processors=8)"

I mean, how to create horse.files then?

Answer 1

[Steven Lakin]

Hello,

The "files" file will need to be created by you in the following format, where each word is separated by a tab:

SampleName     Sample_1.fastq    Sample_2.fastq

You can have as many samples as you want, one on each row with its corresponding fastq files separated by tabs.

For example, if you're in a linux shell, you could do this:

echo -e "SRR952153\tSRR952153_1.fastq\tSRR952153_2.fastq > horse.files

Or use a text editor such as pico or vi:

• pico horse.files
• [add your file information]
• Crtl + x to exit the editor

[flavobacteria]

I use HPC cluster.

echo -e "SRR952153\tSRR952153_1.fastq\tSRR952153_2.fastq > horse.files

I realize the " ahead of SRR952153 and t ahead of other two .fastq are right?

I copy the command, it does not work

Thank you for advice

[flavobacteria]

Hi When you mention about

The "files" file will need to be created by you in the following format, where each word is separated by a tab:

SampleName     Sample_1.fastq    Sample_2.fastq

where can we do it?

and the command like

echo -e "SRR952153\tSRR952153_1.fastq\tSRR952153_2.fastq > horse.files

what the " and t ahead of the seq file stand for? Thank you

Answer 2

[amirmhzadeh]

Use paste:

$whatis paste

paste                (1)  - merge lines of files
paste                (1p)  - merge corresponding or subsequent lines of files