How to make a file that combine the three data files

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?

assembly snp next-gen-sequencing

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updated 3.5 years ago by Ram

• written 11.2 years ago by flavobacteria •

2 answers

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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updated 3.5 years ago by Ram

• written 11.2 years ago by Steven Lakin

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

• 0 views • link

updated 3.5 years ago by Ram

• written 11.2 years ago by 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

• 0 views • link

updated 3.5 years ago by Ram

• written 11.2 years ago by flavobacteria •

Use paste:

$whatis paste

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

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updated 3.5 years ago by Ram

• written 11.2 years ago by amirmhzadeh •