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Old 01-04-2012, 04:00 AM   #2
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 625

Hi antgomo,

As far as Bismark is concerned you could either concatenate the files before the alignments (in the same way you did) or merge the result files, either will be fine. You just need to make sure that the sequences are in the correct order (every single sequence in file_1 must correspond to the other end in file_2) throughout.

so it could look like this:
-1 NB_Lib1_L1_PE250_1.fq,NB_Lib1_L2_PE250_1.fq,NB_Lib1_L3_PE250_1.fq -2 NB_Lib1_L1_PE250_2.fq,NB_Lib1_L2_PE250_2.fq,NB_Lib1_L3_PE250_2.fq

-1 NB_1.fq -2 NB_2.fg (for concatenated files)

Just for the record, as far as I know the pipeline recommended by Illumina uses CASAVA only for their RRBS (do you have RRBS-type libraries?). If you need any additional help with your files (e.g. regarding quality control etc...) please send me an email.
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