Dear Colleagues,One important thing to keep in mind when the new format is used -- the Illumina 'chastity' filter is encoded in the second field of the second word of the header line. In the past, the instrument would remove sequences which failed to pass the filter. Now, those reads are included. You have to decide whether you want to use the additional reads.
Bob Bastien Chevreux wrote:
On Aug 13, 2011, at 20:40 , Peter Cock wrote:Do i have to change all @headers now??Yes, unless Bastien has already updated the latest version of MIRA to cope with the new Illumina 1.8 files.I haven't. Will probably do whenever I encounter a 1.8 pipeline data set for the first time. But I'm still wondering why Illumina made that change in the first place, I cannot find a single good explanation. In the mean time, changing the @-header lines is left as an exercise to the reader :-) B.
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