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Old 09-07-2012, 03:40 PM   #1
czl0020
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Default How to remove adaptor from the NGS data?

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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Old 09-07-2012, 04:00 PM   #2
DZhang
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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
www.contigexpress.com
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Old 09-07-2012, 04:17 PM   #3
SES
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cutadapt is good tool for adapter removal and trimming.
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Old 09-12-2012, 03:09 PM   #4
swNGS
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TrimGalore is a helpful wrapper that works with Cutadapt and FastQC if you want to, for example trim different sequences from each end...
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Old 09-12-2012, 10:21 PM   #5
Huan@illumina.com
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CASAVA 1.8.2 has a built in adapter-masking option that can be called up by using the --adapter-sequence flag. You will need to point it to a fasta file that contains the adapter sequence you want trimmed.
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