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  • SOAP2 (SOAPaligner) -v option

    Our team use SOAP2 to align our read data (human sample).



    During the processing situation, I found that -v option value has no effect to the result & execution time of alignment.

    Here the command usage we wrote.



    soap -v 4 -a $INPUT_FILE -D $REFERENCE_FILE -o $TMP_FILE

    soap2sam.pl $TMP_FILE 1> $OUTPUT_FILE



    We tried to change the -v option value from 0 to 3, but after the soap program is completed we found that the result has the same mapping results.

    By googling about the -v option of SOAP2, we've been told we should use -M option combination with -v option (http://seqanswers.com/forums/showthread.php?t=2411)

    But It seems that the value 1, and 2 of -M option doesn't have the exactly same meaning with "ALLOWED NUMBER OF MISMATCH" but "ONLY THE ALIGNMENT WHICH HAS # MISMATCH(ES)".



    -M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
    0: exact match only
    1: 1 mismatch match only
    2: 2 mismatch match only
    4: find the best hits


    I feel this problem cannot be handled by myself, so I need your explanation or comments.

    What can I do to get the alignment outputs which have differenct number of allowed mismatches?



    Sincerely.
    Last edited by hosang.jeon; 02-23-2012, 07:43 PM. Reason: I wrote a question but I posted it.

  • #2
    Yes please more info on this topic is really necessary.
    what I was told it to use the seed value in -l so then the mismaches will be used from -v

    I just found this: https://groups.google.com/forum/?fro...ap/a-a_Ydmg2r8

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