dear Martin, thank you for your helpful answers!
bests, jo On Fri, Feb 5, 2010 at 6:07 PM, Martin Morgan <[email protected]> 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: [email protected] [email protected] URL: http://bioinfo.i-med.ac.at [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
