I did one lane illumina Hiseq, the output is 400 million reads. The question is there are about 1,800 different adaptors in the raw data file, is there any easy and fast way to remove those 1,800 different adaptors?
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Do you want to simply remove the adapters or sort the reads out based on different adapters and then remove the adapters? Either way, please look into this tool: http://hannonlab.cshl.edu/fastx_toolkit/
Best regards,
Douglas
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