Question: (Closed) Converting Consensus Fastq To Fasta
gravatar for Love
7.4 years ago by
Love100 wrote:

Possible Duplicate:
How to generate a consensus fasta sequence from SAM tools pileup?

How common are multi-line fastq files?

I was trying to convert a fastq consensus sequnece (generated by the mpileup samtools) to a fasta file. However the original FASTQ lines are wrapped. Most of fastq parsers do not work with multi-line fastq files. They only work for 4 lines standard fastq format. Is there a perl script or C# or Java tools to deal with this issue? Please don't use Python, I am not strong on it and I don't want to be an expert on many programming languages during a short time. Of cource, if python is realy powerful, it is considerable.:)

Also if we can get the corresponding quality score for each of the entries, it will be great.


fasta perl fastq • 3.1k views
ADD COMMENTlink modified 7.4 years ago by Swbarnes21.4k • written 7.4 years ago by Love100
gravatar for Swbarnes2
7.4 years ago by
Swbarnes21.4k wrote:

It's not too hard to alter the program itself to make fastas instead of fastqs. perl programs are just ordinary text. You want to find the place where it prints out "@" and sequence, and change the "@" to a ">", and you want to comment out the lines where it prints out the "+", newline, and the quality string, by putting "#" in front of those lines.

That's what I did. I don't have access to it here, but I can pull it up tomorrow. Poke around here or seqanswers for the last time I told someone how to fix the perl script to do that.

Or, you could do it with a short perl script, or maybe a line of sed.

ADD COMMENTlink written 7.4 years ago by Swbarnes21.4k
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