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  • something about my 454 result

    Hello everyone:)
    I have just finish a 454 transcriptome sequencing by FLX-Ti
    The company send me 6 result files:
    454BaseCallerMetrics.txt
    454NewblerMetrics.txt
    Stressed_454Reads.zip
    Stressed_454AllContigs.zip
    Control_454Reads.zip
    Control_454AllContigs.zip
    I wonder if these are complete results. Because I see some paper say some
    SFF files and .qual.
    Shall I ask the company to send me more files? For example? someone help me ,thank you

  • #2
    May some experienced people tell me what other files I should ask the company for to do the later detailed analysis? I am a newly learner in this filed.

    Comment


    • #3
      Hi,

      I suspect that you'll find either a .sff or your .fna and .qual files if you unzip the .zip files. WinRar (www.rar-lab.com) is pretty good, but if you're using Windows you should just be able to double click the files and Windows will extract them for you.

      Cheers,
      Rachel

      Comment


      • #4
        yes I would expect that you have your raw reads in the files "Stressed_454Reads.zip" and "Control_454Reads.zip" probably as .fna and .qual
        The .fna file is the sequences in .fasta format and the .qual file will contain the quality valves for each base. These files should be significantly bigger than the others. The "allcontig" files will contain contigs produced from your reads using the 454 Newbler software.
        Good luck

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        • #5
          Thank you rglover and Adams
          I have unzip the 4 files above,I got
          2.TCA.454Reads.fna
          1.TCA.454Reads.fna
          stress454AllContigs.fna
          stress454AllContigs.fna
          But I found no qual files. So what do you think about the files? Are there any other files I need?

          Comment


          • #6
            thank you

            thank you I have reply in my thread
            please have a look

            Comment


            • #7
              Hi,

              You'll have to contact the sequencing company if they haven't included the quality files in with your sequences. You'll only get quality files which match the reads inside the .fna files - you won't get quality files for the contigs.

              As a polite request, could you not send PMs if people haven't replied to your thread in a matter of hours? I check the forum at least once a day but I'm not here constantly - it's a little annoying to get a PM that essentially says "please respond to my thread".

              Comment


              • #8
                Really sorry to bother you rglover, but thanks a lot for your help
                I will take your words next time.

                Comment


                • #9
                  You want the SFF files, ideally.

                  Comment


                  • #10
                    You will *need* SFF files if you submit your data to NCBI (e.g. for publication isues)

                    Comment


                    • #11
                      HELLO Tangsha
                      can you leave a communication way to me? I want to ask you some questions about 454 sequencing. now i am in ,Sun yat-sen university,Guangzhou .

                      my QQ:409517906
                      Email: [email protected]

                      Comment

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