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  • cutcopy11
    Member
    • Nov 2009
    • 19

    quick basic questions about csfasta.ma.25.2 files

    I am looking at some other people's processed data at GEO but I am unclear
    about the alignment meanings.

    Some information about *csfasta.ma files is found in the following guide:
    Thermo Fisher Scientific enables our customers to make the world healthier, cleaner and safer. Delivering technology, pharmaceutical and biotechnology services.


    However, I have some questions that were not answered in the manual with
    the exception of question #2.

    Here is a sample alignment from a single-read, SOLiD csfasta.ma.25.2 file.
    T30211102000121023203110321200211210
    2_16_1134_F3,chr12.-97446261.1,chr12.75715114.1,chr14.92697281.1


    1.
    Does the negative sign in front of the chromosomal coordinate indicate a reverse read (- strand)?
    2.
    Does the .1 in these 3 alignments indicate the number of mismatches as in 1 mismatch each?
    3.
    For the forward reads, does the coordinate represent the 5' end (the left-most coordinate)?
    4.
    For the reverse reads, does the coordinate represent the 3' end (the left-most coordinate)?
    5.
    If the answer to #4 is yes, to obtain the 5' end of the reverse read,
    should I add 25 to the coordinate?
    For example, to obtain the 5' end of the read in the "chr12.-97446261.1" alignment,
    would this be the appropriate operation: 97446261 + 25 = 97446286?
    Or should I add 24?

    Thanks,
    Clayton

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