dear all,

this is probably a very simple question but i'm quite new to the high
throughput sequencing...
I've got reads from an ChIPseq experiment and the service provider sent me
finally also the list of adaptors and primers for which i want to screen and
clip the reads (using the trimLRPatterns function from the ShortRead package
).

my question now is if I have to reverse complement the sequences also, and
if I should use e.g. the DNA_AD1 as the Lpattern parameter and the DNA_AD2
as the Rpattern, or how does this work now? below I pasted some of the
adaptor/primer sequences.

sorry for my newbie-question,

bests, jo


>DNA_AD1
GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG
>DNA_AD2
ACACTCTTTCCCTACACGACGCTCTTCCGATCT
>DNA_PCR1
AATGATACGGCGACCACCGACACTCTTTCCCTACACGACGCTCTTCCGATCT
>DNA_PCR2
CAAGCAGAAGACGGCATACGACGCTCTTCCGATCT
>DNA_SEQ
CACTCTTTCCCTACACGACGCTCTTCCGATCT
>GEXD_AD11
GATCGTCGGACTGTAGAACTCTGAAC
>GEXD_AD12
ACAGGTTCAGAGTTCTACAGTCCGAC
>GEXD_AD21
...


-- 
Johannes Rainer, PhD
Bioinformatics Group,
Division Molecular Pathophysiology,
Biocenter, Medical University Innsbruck,
Fritz-Pregl-Str 3/IV, 6020 Innsbruck, Austria
and
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria

Tel.:     +43 512 570485 13
Email:  johannes.rainer@i-med.ac.at
           johannes.rainer@tcri.at
URL:   http://bioinfo.i-med.ac.at

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