This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Converting Consensus Fastq To Fasta

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.

Thanks.

fastq fasta perl
• 4,328 views • link
updated by Swbarnes2 Swbarnes2 • written by Love • Love

1 answer

It's not too hard to alter the samtools.pl 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.

• 1 views • link
written by Swbarnes2 Swbarnes2

Log in to answer this question.

More posts like this
  • How Is Heterozygosity Determined In A Consensus Fasta?
    written by Justin Justin
    <p>I have a consensus fasta file generated by <a href='http://samtools.sourceforge.net/'>samtools</a>/bcftools/vcfutils as discussed in a previous post here: <a href='/p/1388/'>How to generate a consensus fasta sequence …
  • How To Generate A Consensus Sequence On The Galaxy Platform
    written by thelittledoctor • thelittledoctor
    <p>Greetings,</p> <p>I am attempting to generate a consensus sequence using the galaxy platform. I have been able to generate a pileup using Mpileup however I …
  • What Is The Minimum Quality Score
    written by Love • Love
    <p>Hello, I just created a fastq file from samtools. Now I want to do some kinds of quality things since I am not confident the …
  • How To Pull Out Qual From Multi Line Fastq?
    written by Zhshqzyc • Zhshqzyc
    <p>From <a href="http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consensus-fasta-sequence-from-sam-tools-pileup">http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consensus-fasta-sequence-from-sam-tools-pileup</a> We use awk and perl to get fasta by</p> <pre><code>awk '/^@chr1$/,/^+$/' consensus.fastq | perl -pe "s/@/&gt;/ ; s/\\+//" &gt; chr1.fasta </code></pre> <p>The …
  • Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fixing Explanations
    written by Delinquentme Delinquentme
    <p>So I've read a few threads on here... and it seems that there are quite a few questions about what SPECIFICALLY makes up a hidden …
  • Know Of Any Personal Fellowships, But Not Postdoctoral Positions, In Bioinformatics?
    written by Mach • Mach
    <blockquote> <p><strong>Possible Duplicate</strong>: <a href="http://biostar.stackexchange.com/questions/7709/post-doctoral-fellowships-in-bioinformatics-computational-biology">http://biostar.stackexchange.com/questions/7709/post-doctoral-fellowships-in-bioinformatics-computational-biology</a></p> </blockquote> <p>Hello,all. Could you please, give me some advise and links, how to get a personal fellowship in bioinformatics. I …
  • Best Directory Tree To Organize Ngs Data On A Shared Server
    written by Nicolas Rosewick Nicolas Rosewick
    <blockquote> <p><strong>Possible duplicate</strong>: <a href="http://biostar.stackexchange.com/questions/822/how-do-you-manage-your-files-directories-for-your-projects">http://biostar.stackexchange.com/questions/822/how-do-you-manage-your-files-directories-for-your-projects</a></p> </blockquote> <p>Hi,</p> <p>My lab recently received a new server. We're now thinking on how organize the data and results on …
  • Can Bam File Be Converted To Fasta Format?
    written by Hmm • Hmm
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/6993/convert-bam-file-to-fasta-file">Convert bam file to fasta file</a> </p> </blockquote> <p>Can we convert a whole human genome bam file into fasta format. …
  • Extract A Sequence From Ucsc
    written by Litali • Litali
    <blockquote> <p><strong>Possible Duplicate:</strong> <br/> <a href="http://biostar.stackexchange.com/questions/56/how-to-get-the-sequence-of-a-genomic-region-from-ucsc">How to get the sequence of a genomic region from UCSC?</a> </p> </blockquote> <p>Hello, I want to receive the sequence …
  • How To Generate A Consensus Fasta Sequence From Sam Tools Pileup?
    written by Casey Bergman Casey Bergman
    <p>SAM tools pileup produces a consensus sequence in vertical format, which is not terribly useful for traditional sequence analysis. Does anyone know of a command …