dear Martin,

thank you for your helpful answers!

bests, jo

On Fri, Feb 5, 2010 at 6:07 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Jo --
>
> On 02/04/2010 10:20 PM, Johannes Rainer wrote:
> > 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.
>
> Not a direct answer to your question, but ... (a) Solexa reads are
> reported as read from the flow cell, 5' to 3'; I think this means that
> no reverse complement is necessary. (b) I think it's relatively unusual
> to trim or filter ChIP-seq Solexa reads -- at least in shorter reads
> trimming would mean that there wasn't enough sequence for alignment, and
> not trimming would mean that the sequence is too dissimilar for
> alignment in the first place. Either way you end up with adapter
> sequences not aligning, and hence being discarded from any downstream
> analysis.
>
> Trimming adapters might become important in other scenarios, e.g., miRNA
> where the target is shorter than the read, or working with longer reads
> where sample prep introduces artifacts to be removed (e.g., primers or
> bar codes in metagenomic analysis of 454 reads).
>
> Martin
>
> > 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
> > ...
> >
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
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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