Hi,
I am working on transcript quantification, where multi-reads, i.e. reads which can be mapped to multiple locations within a transcript/genome, is an important issue as such multi-reads add ambiguity to transcript counts.
Although longer reads can have a better chance to be mapped uniquely to a genomic location, I am concerned about read error for longer reads. Specifically, does the number of errors within a read increase linearly with read length, or not?
For example, if a 80bp read will contain 1 error on average, then is it fair to assume a 160bp read will contain 2 errors on average, or actually more?
As far as I know, read quality deteriorates from the 5' end to the 3' end, hence errors occur more often at the 3' end. Suppose the low quality 3'end begins in the middle of a 80bp read (i.e. the 41bp from the 5'end), can I assume the low-quality end for a 160bp read also will start in the middle (i.e. the 81bp from the 5'end), or will it still start at the 41bp of the read?
Please suggest. Thanks in advance.
Billy
I am working on transcript quantification, where multi-reads, i.e. reads which can be mapped to multiple locations within a transcript/genome, is an important issue as such multi-reads add ambiguity to transcript counts.
Although longer reads can have a better chance to be mapped uniquely to a genomic location, I am concerned about read error for longer reads. Specifically, does the number of errors within a read increase linearly with read length, or not?
For example, if a 80bp read will contain 1 error on average, then is it fair to assume a 160bp read will contain 2 errors on average, or actually more?
As far as I know, read quality deteriorates from the 5' end to the 3' end, hence errors occur more often at the 3' end. Suppose the low quality 3'end begins in the middle of a 80bp read (i.e. the 41bp from the 5'end), can I assume the low-quality end for a 160bp read also will start in the middle (i.e. the 81bp from the 5'end), or will it still start at the 41bp of the read?
Please suggest. Thanks in advance.
Billy
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