Hi,
I am using DataAnalysis_2.6_All_20110523_1850 gsMapper to map some reads to the sequences they come from, so that I know the original position of the reads.
The thing is that for some sequences starting with an homopolymer the BAM file outputs a wrong position while in 454PairAlign it is correct. I think is happening something like:
BAM file:
AAAAAA-----------------------AGTCGGCTAGCGATGCGA
AAAAAAAAAAAAAAAAAGTCGGCTAGCGATGCGA
454PairAlign
______________AAAAAAAGTCGGCTAGCGATGCGA
AAAAAAAAAAAAAAAAAAGTCGGCTAGCGATGCGA
I have searched for this discussion but haven't found anything. Has anyone information about this issue? I am about to write Roche about this bug, cause could be really error prone when working with sequences without knowledge of their actual position, when using the BAM file. But I wanted to ask here before to do that cause likely I am missing something.
thank you
I am using DataAnalysis_2.6_All_20110523_1850 gsMapper to map some reads to the sequences they come from, so that I know the original position of the reads.
The thing is that for some sequences starting with an homopolymer the BAM file outputs a wrong position while in 454PairAlign it is correct. I think is happening something like:
BAM file:
AAAAAA-----------------------AGTCGGCTAGCGATGCGA
AAAAAAAAAAAAAAAAAGTCGGCTAGCGATGCGA
454PairAlign
______________AAAAAAAGTCGGCTAGCGATGCGA
AAAAAAAAAAAAAAAAAAGTCGGCTAGCGATGCGA
I have searched for this discussion but haven't found anything. Has anyone information about this issue? I am about to write Roche about this bug, cause could be really error prone when working with sequences without knowledge of their actual position, when using the BAM file. But I wanted to ask here before to do that cause likely I am missing something.
thank you
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