Originally posted by fkrueger
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You should ask whoever is doing the sequencing for you what to expect in terms of read quality towards the end of the reads. When we were sequencing with the GA, we had extremely high quality all the way to base 100 -- often a median > Q35.
With the hiseqs they have been optimizing some things. We have had some runs "fail"... but they were eventually redone, and typically we have quality >Q30 at read 100. Especially since you expect to have many mismatches, I think that the value of longer reads would be very high for your application. You can always quality trim your reads using a tool like fastx (fastq_quality_trimmer). Even when the quality trails off at the end of a run, you will get a large fraction of the reads that don't need to be trimmed.
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Thanks All for the informative answers.
Hi all I have another Question regarding this approach:
Q2) Secondly a concern some of my colleagues have highlighted is that using a PCR approach we would get over-representation of the start and end of the reads (i.e. the start and end of the desired 200bp amplicon) and a much lower if not absent coverage of the middle portion. Would anyone have any comments as to whether this would be the case and if so are there ways around this?
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