converting fasta/fa files to fastq

kaps · 05-22-2015, 05:04 AM

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?

GenoMax · 05-22-2015, 05:17 AM

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

GenoMax · 05-22-2015, 05:20 AM

Quote:

Originally Posted by kaps

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

kaps · 05-22-2015, 05:54 AM

Quote:

Originally Posted by GenoMax

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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05-22-2015, 05:04 AM	#1
kaps Member Location: Uganda Join Date: Jan 2015 Posts: 71	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?

05-22-2015, 05:17 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,082	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