I am wondering whether cluster registration occurs for read 2 of Illumina paired end sequencing? I know that having a common sequence at the start of read 1 would not enable cluster registration to occur, but do not know if there would be a similar problem if read 2 began with a common sequence such as a polyA stretch of about 10 bases in every cluster.
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I believe cluster recognition happens just once, at the beginning of the first read. -
Beware though, there may be focus problems for your read 2 if all the signal is coming from one (A) channel.Comment
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Thank you for the responses, TonyBrooks can read 2 recover from focus issues encountered at the start of the read?Comment
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Hi plinko
There is no cluster registration in read 2 but there is a matrix generation step for that you don't want intensity from only one base. There will not be focus problem. It is not clear which platform you are using for sequencing if it is GA IIx there is no calibration step at all. In hiseq and MiSeq there is calibration but it will not affect if u have only one base but, first to start imaging one lane in flowcell must have clusters with base G or T.Comment
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