Hi, Does anyone know the sequencing error rates in Illumina platform?
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Originally posted by sixguns View PostIf my data is 75bp not strand, it means that it close to 1bp error per read?
HOWEVER I think the Illumina error rate may be misleading us. I believe they only count MAPPABLE reads to their PHIX74 CONTROL. Now, a read which has lots of errors will NOT MAP, hence will not count toward the error rate! Simply by tweaking their mappability thresholds, they can choose any error rate they want to match a reasonable yield...
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Yes but how can you calculate the 'true' errors rate, meaning the level of misreading, the level of chimeria, etc... For that you must know perfectly your DNA you are sequencing, and you cannot, due to continual modification of it... However, you can estimate it based on the common sequences between reference and tested sequences, and in calculating the false of non-SNP mismatches /indels.
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Originally posted by cdry7ue View PostFrancois, is there a paper/document describing in more details the suggestions you just gave above. I have DNA which we prepared by doing PCR on a normal individual,confirmed size by CE and also are planning to do Sanger sequencing.
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