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Old 05-22-2015, 04:04 AM   #1
kaps
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Location: Uganda

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Default converting fasta/fa files to fastq

Hello I seen a script on this link https://code.google.com/p/fasta-to-fastq/ that converts fasta to fastq either as standalone or unix workflow.

How can use I it either as standalone or unix?
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Old 05-22-2015, 04:17 AM   #2
GenoMax
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You can use reformat.sh from BBMap to assign fake Q-scores to a fasta file to convert it to fastq.

Code:
$ reformat.sh in=test.fa out=fake.fq qfake=35
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Old 05-22-2015, 04:20 AM   #3
GenoMax
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Quote:
Originally Posted by kaps View Post
Hello I seen a script on this link https://code.google.com/p/fasta-to-fastq/ that converts fasta to fastq either as standalone or unix workflow.

How can use I it either as standalone or unix?
You can download the script from here: https://code.google.com/p/fasta-to-f...ta_to_fastq.pl Use wget or curl with this link: https://fasta-to-fastq.googlecode.co...ta_to_fastq.pl

Code:
$ wget https://fasta-to-fastq.googlecode.com/files/fasta_to_fastq.pl
Add execute permissions to it on server

Code:
$ chmod u+x fasta_to_fastq.pl
And then run it
Code:
$ perl fasta_to_fastq.pl reads.fasta > my_converted_fasta.fq
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Old 05-22-2015, 04:54 AM   #4
kaps
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Location: Uganda

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Quote:
Originally Posted by GenoMax View Post
You can download the script from here: https://code.google.com/p/fasta-to-f...ta_to_fastq.pl Use wget or curl with this link: https://fasta-to-fastq.googlecode.co...ta_to_fastq.pl

Code:
$ wget https://fasta-to-fastq.googlecode.com/files/fasta_to_fastq.pl
Add execute permissions to it on server

Code:
$ chmod u+x fasta_to_fastq.pl
And then run it
Code:
$ perl fasta_to_fastq.pl reads.fasta > my_converted_fasta.fq
its working well

Thanks
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