Ok so I am a newbie here, so please bear with me. I am trying out Bowtie. And following the manual and I issue the command as it is in the manual (I just removed the --suppress 1,5,6,7 to make all the columns visible.
./bowtie -a -v 2 e_coli -c ATGCATCATGCGCCAT
The first two lines of the output are as follows...
0 - gi|110640213|ref|NC_008253.1| 148810 ATGGCGCATGATGCAT IIIIIIIIIIIIIIII 0 10:A>G,13:C>G
0 - gi|110640213|ref|NC_008253.1| 2852852 ATGGCGCATGATGCAT IIIIIIIIIIIIIIII 0 8:T>A
If I am reading this right, it found matches on the negative reference strand, with TWO mismatches on the first result (10:A>G,13:C>G). But when I look at the alignments closely,
Test - ATGCATCATGCGCCAT
Result 1 - ATGGCGCATGATGCAT
I see mismatches at position 4,5,6,11,12,13.
Same thing with result TWO
Test - ATGCATCATGCGCCAT
Result 1 - ATGGCGCATGATGCAT
Bowtie says ONE mismatch in position 8, while I see mismatches in positions 4,5,6,11,12,13
What AM I missing here? Please apologize for relative ignorance of the question.
Thanks
Quantrix
./bowtie -a -v 2 e_coli -c ATGCATCATGCGCCAT
The first two lines of the output are as follows...
0 - gi|110640213|ref|NC_008253.1| 148810 ATGGCGCATGATGCAT IIIIIIIIIIIIIIII 0 10:A>G,13:C>G
0 - gi|110640213|ref|NC_008253.1| 2852852 ATGGCGCATGATGCAT IIIIIIIIIIIIIIII 0 8:T>A
If I am reading this right, it found matches on the negative reference strand, with TWO mismatches on the first result (10:A>G,13:C>G). But when I look at the alignments closely,
Test - ATGCATCATGCGCCAT
Result 1 - ATGGCGCATGATGCAT
I see mismatches at position 4,5,6,11,12,13.
Same thing with result TWO
Test - ATGCATCATGCGCCAT
Result 1 - ATGGCGCATGATGCAT
Bowtie says ONE mismatch in position 8, while I see mismatches in positions 4,5,6,11,12,13
What AM I missing here? Please apologize for relative ignorance of the question.
Thanks
Quantrix
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