I have a FASTA file, how can i convert it to a FASTQ file via command line or by any online converter. The existing online converter is giving error and is unable to parse my fasta file.
The FastQ formats contains, in addition to the sequence information, also information on the quality of the sequencing read (see http://maq.sourceforge.net/fastq.shtml). In contrast, the FastA format contains only the sequence information and lacks the quality information. Therefore, you cannot produce a proper FastQ file from a FastA file.
(You could produce dummy FastQ files with the real sequence and a constant dummy quality score score for each position)
The FastQ formats contains, in addition to the sequence information, also information on the quality of the sequencing read (see http://maq.sourceforge.net/fastq.shtml). In contrast, the FastA format contains only the sequence information and lacks the quality information. Therefore, you cannot produce a proper FastQ file from a FastA file.
(You could produce dummy FastQ files with the real sequence and a constant dummy quality score score for each position)
you could use things like ART (https://www.niehs.nih.gov/research/resources/software/biostatistics/art/) and there is also a command in EMBOSS i dont remember the name. they take a fasta in and give fastq out
If you have not made fasta from fastq yourself (and you dont have qual data) YOU CAN NOT.
So how could I convert the reference fasta for the human mitochondrion into two fastq files that then I aligned with BWA?
You import reference sequences into BWA in fastA format
http://bio-bwa.sourceforge.net/bwa.shtml
sorry, I wasn't clear: I converted the fasta file of the human mitochondrion into two paired fastq files. ART provides a simulated quality profile that is fed into the fastq files.
Annemarie Honegger Hi! I saw that Luigi did not get the point that fasta can't be converted to fastq to be used in any practical use except for the simulation studies. But I did not get the point how did you suggest to use BWA tool to get fastQ output from fastA input, even using a reference genome in fastA fomat.
@Abhijeet Singh, I was not suggesting to use BWA to convert fastA to fastQ, but referring to the fact that in order to align sequencing reads to a reference sequence in BWA, you import the reference sequence in fastA format and the sequencing reads in fastq format, making it unnecessary to convert the reference sequence.
There is a perl script.
Download the script from here: https://code.google.com/p/fasta-to-f...ta_to_fastq.pl
1)Use wget or curl to download it.
wget https://fasta-to-fastq.googlecode.com/files/fasta_to_fastq.pl
2 ) Get permission.
chmod u+x fasta_to_fastq.pl
3)run it
perl fasta_to_fastq.pl reads.fasta > my_converted_fasta.fq
Yes Prithvi Singh , you can convert FASTa files to FASTq files.
You can use bbmap suite to do it, it works better for us, use it like this:
reformat.sh in=file.fasta out1=file_R1.fastq out2=file_R2.fastq qfake=40 fastareadlen=150 qout=33 addcolon=t trimreaddescription=t uniquenames=t
You can modified fastareadlen to set read length and qfake to set base quality scores, more options you can check reformat.sh --help
Best,
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