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  • TCA.454reads.fna

    Do you know if the file TCA.454reads.fna contains the "raw" reads, everything that it has been sequenced during a run (even short reads, etc)? Can I imput this file to an aligner software instead of the. sff file that I can extract after AVA alignment? Thank you in advance

  • #2
    I can go to terminal and type touch TCA.454reads.fna and I can tell you with 100% confidence that my TCA.454reads.fna file will not contain "raw" reads or anything else for that matter..
    savetherhino.org

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    • #3
      So it contains only the good quality reads?

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      • #4
        Originally posted by CCBIO View Post
        So it contains only the good quality reads?
        What I mean is that how could we possibly know what your file contains. It's like asking what some random .docx file in my Documents folder contains..
        savetherhino.org

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        • #5
          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


          That should be the raw data in fasta format for a specific region (indicated by the number in the file name before TCA).

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          • #6
            It's all of the reads that passed the filters. It contains all of the same reads as the .sff file; the difference is that the .fna file contains only the trimmed sequence information rather than all of the quality, and trim information.

            If you want different information than that, you can use the command line tools (sfffile, sffinfo, etc.) to get different information out of the .sff file (untrimmed reads, read subsets, quality information, rescore the reads, and more).

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            • #7
              Thank you!

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