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Old 03-19-2014, 02:04 PM   #6
sprocha
Junior Member
 
Location: spain

Join Date: Mar 2014
Posts: 2
Default adaptor sequences

Hi,
I may have a very stupid question here... new to this...
I just got my reads and checked (fastQC) that among the "overrepresented sequences" are full adaptors (universal and indexed, 100% over 50bp, so I assume it's the complete thing...)

I see that the adaptor sequences that people usually use are shorter, the inner fragments of these... and when I use only those, yes, these "overrepresented" sequences are not there anymore. I used trimmomatic with cmd ILLUMINACLIP:Cadaptor31.fa:1:30:10:8:true giving adaptor file:

>PrefixPE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT # this being the 3' end of the TruSeq Universal adaptor (5'-3')
>PrefixPE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC # this being the 3' end of the TruSeq Indexed adaptor (5'-3')
>PE/1
TACACTCTTTCCCTACACGACGCTCTTCCGATCT # this being the 3' end of the TruSeq Universal adaptor (5'-3')
>PE/1_rc
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
>PE/2
GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC # this being the 3' end of the TruSeq Indexed adaptor (5'-3')
>PE/2_rc
GATCGGAAGAGCACACGTCTGAACTCCAGTCAC


what is trimmomatic doing exactly?? when it detects an adaptor, it removes it until its 3' end...? if not I still should be seeing the remaining parts as overrepresented, right??

should I give it instead an adaptor file with the full sequences?

many thanks in advance,
sara
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