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.
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.
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