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fastq to fasta conversion
How can I convert my fastq files to two fasta files with one containing the reads and another containing the quality scores?
Thanks
Thanks
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You could use awk to create a simple fasta file from your fastq, e.g.
awk 'NR % 4 == 1 {print ">" $0 } NR % 4 == 2 {print $0}' my.fastq > my.fasta
However, I don't think it makes any sense to create a fasta file "containing the quality scores". Fasta files are used to represent sequences. -
... and their corresponding qualities ..Originally posted by Bio.X2Y View Post
mySeq.fasta :
>mySeq
ACGTACGT
mySeq.fasta.qual:
>mySeq
22 22 33 33 22 22 33 44
There are still some programs which need to be fed with fasta/qual :-)
Anyway, qualities need to be converted to phred-stye ..Comment
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Thanks sklages! I wasn't aware of qual files.
kwtennis311, there seem to be some existing posts on this, you might find answers in this, e.g. http://seqanswers.com/forums/showthread.php?t=3730.Comment
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thanks
thanks guys, Biopython did the trickComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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