How to make a file that combine the three data files
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7.2 years ago

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?

next-gen Assembly sequencing SNP • 2.5k views
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Entering edit mode
7.2 years ago
Steven Lakin ★ 1.8k

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

 

 

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7.2 years ago

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

 

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Entering edit mode
7.2 years ago

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

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7.2 years ago
amirmhzadeh ▴ 80

Use paste:

$whatis paste

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

 

 

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