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  • seq.txt, qseq.txt and fastq

    Hi,

    What is the difference betweend seq.txt format, qseq.txt format and fastq format ?

    Thanks

    N.

  • #2
    As I know, the difference between fastq format and fasta format is that each base in the fastq file has a quality value which can tell you whether the base call is reliable.The fasta format discard this quality value information.

    I hope it will help you.

    Comment


    • #3
      .fastq and .txt files

      Hi
      I have kind of similar question- I am not clear what is the difference in seq file .fastq and .txt file of same seq. The problem I have is our inhouse run normally use .txt file When I check fastq file and .txt file they appear to be same.


      Am i missing something.
      Thanks


      here is snap shot of .txt
      @HWI-ST550_0128:8:1101:1400:2026#CCGTCC/1
      NTTTTCAAAATAGCAAAAACTCTTTGAAGTTAAACATTAAGAAAATGCTAA
      +HWI-ST550_0128:8:1101:1400:2026#CCGTCC/1
      BP\cceeegggggihhiiiiiiiiiheggiiiiiiihiiihiihiiiiiif
      @HWI-ST550_0128:8:1101:1297:2085#CCGTCC/1


      and fastq

      @HWI-ST550_0128:8:1101:1187:2009#ATGTNN/1
      NGTTTGTTTGAATTTATGAGTTAGGTCCATCAACCTAGGCTGATATTNNGA
      +HWI-ST550_0128:8:1101:1187:2009#ATGTNN/1
      BP\cceceggeeehhfgheghghihgihhhgfgfgd^eghhhegffhBBBB
      @HWI-ST550_0128:8:1101:1162:2025#AGTTNN/1
      NTACATTTATAATGTAACATGTGTAACATTATACACATATCTCTTTGNNTC
      +HWI-ST550_0128:8:1101:1162:2025#AGTTNN/1
      Last edited by mathew; 05-21-2012, 08:42 AM.

      Comment


      • #4
        fastq is just a type of text file. It refers to the format of the sequence data, which looks fine in your examples.

        Comment


        • #5
          Anybody know how to convert qseq to fasta or fastq?
          thanks!

          Comment


          • #6
            From the QIIME manual (easily found via a web search):

            You can convert qseq files to fastq files using the process_qseq.py script.

            Comment

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