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  • Short-reads in FASTA format

    Hi,

    I need to run some experiments on short-reads in fasta format. However, all the sources I found is using FASTAQ format for short-reads. I tried some tools for converting FASTAQ to FASTA, but still having problems with the converted files.

    Could you please point me to sources where I can download short-reads (small files for testing purposes only) in fasta format?

    Thanks.

  • #2
    Very few places will have those available, as almost all aligners are designed to work with FASTQ data, and all modern short-read sequencers only output FASTQ. However, since I assume you're just trying out your own alignment programs, this short python script I whipped up should convert FASTQ to FASTA pretty easily (run it with an input FASTQ file as an argument, make sure the file isn't gzipped first):
    Code:
    #!/usr/bin/python
    import re, sys
    
    try:
        filename = sys.argv[1]
    except:
        exit('Need to supply an input file!')
    
    f = open(filename)
    counter = 0
    for line in f:
        counter = 1 if counter == 4 else counter+1
        if counter == 1:
            print '>'+re.sub(r'>','',line)[1:].rstrip()
        elif counter == 2:
            print line.rstrip()
    If for whatever reason this isn't working for you, let me know and I'll run it on one of my FASTQ files here and e-mail you the result.

    Comment


    • #3
      Thanks a lot for your help. I found some tools to convert from FASTAQ to FASTA.

      Comment

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