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  • know the reads are paired ends via the dataset?

    How could I know the reads are paired ends via the dataset?

    Sometimes, I saw the database looks like


    seq743_A01_F_F01.ab1
    seq743_A01_R_F01.ab1
    ...
    ...

    Are those Roche/454 dataset?

    Another: are they paired-end reads?

    Thanks
    Last edited by arkilis; 09-29-2013, 04:14 PM.

  • #2
    You cannot say anything for sure, just looking on file names. Files are constantly misnamed.
    But, guessing from the filenames:
    No, those are not 454 reads. The ab1 file format is short for AppliedBiosystems, so originates from one of their machines.
    Yes, those are paired-end. At least you can read the _F_ as forward and _R_ as reverse.

    Comment


    • #3
      Originally posted by sBeier View Post
      You cannot say anything for sure, just looking on file names. Files are constantly misnamed.
      But, guessing from the filenames:
      No, those are not 454 reads. The ab1 file format is short for AppliedBiosystems, so originates from one of their machines.
      Yes, those are paired-end. At least you can read the _F_ as forward and _R_ as reverse.
      Thanks, now I already know they are from Sanger. But is there any way to tell the sequencer just from the data set? cheers,

      Comment


      • #4
        Your best guess is to ask whoever sequenced it. There should be information solving all your questions given to you as an information sheet.
        If you got it from a database like NCBI-SRA or such, there is "experiment" information that usually lists the platform used.

        Comment


        • #5
          Originally posted by sBeier View Post
          Your best guess is to ask whoever sequenced it. There should be information solving all your questions given to you as an information sheet.
          If you got it from a database like NCBI-SRA or such, there is "experiment" information that usually lists the platform used.
          Yeah, you are right. Best to get from the manifest.

          Comment

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