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: [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
