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Old 04-07-2014, 10:58 AM   #1
figo1019
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Location: germany

Join Date: Jun 2012
Posts: 32
Default Adapter trimming

Hi

I have got the adapter sequences from company as for Illumina RNA seq data:
5-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC-(insert)-ACCTTAAGAGCCCACGGTTCCTTGAGGTCAGTGXXXXXXTAGAGCATACGGCAGAAGACGAAC-3

(ID #1 "ATCACG" )

Will this be my adapter sequences to trim it using trimmomatic?
>adpter1
AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC
>adapter2
ACCTTAAGAGCCCACGGTTCCTTGAGGTCAGTGATCACGTAGAGCATACGGCAGAAGACGAAC

or I have to reverse complement the adapter ?

Best Regards
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Old 04-07-2014, 11:58 AM   #2
mastal
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Default

Have a look at the TruSeq adapter files that come with trimmomatic,
and see how they compare to the sequences you have.
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