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Old 12-12-2013, 06:07 PM   #8
arcolombo698
Senior Member
 
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default Making the ILLUMINA adapter.fa file

Hello.

Thank you so very much for your response.


The letter from illumina is given to the users as

TruSeq Universal Adapter
5 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Adapter, Index 1 5
5 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG



So based on what you are saying would I create the file as :

>Universal Adapter 5
>AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>TruSeq Adapter, Index 1 5 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG



I am concerned about "whitespace" issues... because I am not sure if I should save the file as :

TruSeq Universal Adapter
>5 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
TruSeq Adapter, Index 1
>5 GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG



my last question, is that ILLUMINACLIP requires adapter.fa.... but you suggest to save as .txt ?

Could you post a clip of your adapter.fa so I can see how to format correctly?


Thanks again

(my other option is to update Trimmomatic from version .22 to version .32)
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