Hi,
I have a question concerning the maq rmdup command file that remove pairs with identical outer coordinates. With the solexa pipeline version 1.3, the name of the reads are not a unique string, i.e., for two different runs we can find different reads with the same name.
My question is, does this affect the maq rmdup command, such that it dumps out all the reads that have the same name? I went through the code of the rmdup.cc script file from the alignment program MAQ but I am not sure how, and if it is affected by this.
Regards,
João
I have a question concerning the maq rmdup command file that remove pairs with identical outer coordinates. With the solexa pipeline version 1.3, the name of the reads are not a unique string, i.e., for two different runs we can find different reads with the same name.
My question is, does this affect the maq rmdup command, such that it dumps out all the reads that have the same name? I went through the code of the rmdup.cc script file from the alignment program MAQ but I am not sure how, and if it is affected by this.
Regards,
João
