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-   -   converting fasta/fa files to fastq (http://seqanswers.com/forums/showthread.php?t=58790)

kaps 05-22-2015 04:04 AM

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?

GenoMax 05-22-2015 04:17 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 04:20 AM

Quote:

Originally Posted by kaps (Post 173077)
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 04:54 AM

Quote:

Originally Posted by GenoMax (Post 173080)
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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