Hi, Perhaps the package CSAR could be useful for you. It is the package used for the analysis of several ChIP-seq experiments in plants (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671559/ ). Starting with the mapped reads, you can obtain a wig file to visualize the read-enrichment with a genome browser (eg: IGB), and to locate the peaks relative to the start and end of Arabidopsis genes.
Greetings, Jose -----Mensaje original----- De: [email protected] en nombre de [email protected] Enviado el: lun 08/02/2010 15:59 Para: [email protected] CC: [email protected] Asunto: [Bioc-sig-seq] Annotation of ChIP-Seq peaks Dear bioc-sig-sequencing, 1. I would like to annotate (& graphically display in context of genome annotation) ChIP-Seq peaks found using Arabidopsis samples. Can someone comment on practical way(s) to do this? 2. For example, would the following be an appropriate approach: a. Employ ChIPpeakAnno package? b. For my ChIPSeq peaks data, would format as RangedData as page 10 of BasicChIPSeq.pdf handout for 11/19/09 talk of M. Morgan (for Nov. 18-20 conference, Seattle)? 2. Can you comment on the error message below? > library(ChIPpeakAnno) ... > library("biomaRt") > listMarts() biomart 1 ensembl 2 snp 3 functional_genomics 4 vega 5 msd 6 bacterial_mart_3 7 fungal_mart_3 8 metazoa_mart_3 9 plant_mart_3 ... version 1 ENSEMBL 56 GENES (SANGER UK) 2 ENSEMBL 56 VARIATION (SANGER UK) 3 ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK) 4 VEGA 36 (SANGER UK) 5 MSD PROTOTYPE (EBI UK) 6 ENSEMBL BACTERIA 3 (EBI UK) 7 ENSEMBL FUNGAL 3 (EBI UK) 8 ENSEMBL METAZOA 3 (EBI UK) 9 ENSEMBL PLANT 3 (EBI UK) ... > mart = useMart("plant_mart_3") > listDatasets(mart) dataset description 1 sbicolor_eg_gene Sorghum bicolor genes (Sbi1) 2 bdistachyon_eg_gene Brachypodium distachyon genes (Brachy1.0) 3 alyrata_eg_gene Arabidopsis lyrata genes (Araly1) 4 oindica_eg_gene Oryza sativa indica group genes (2005-01-BGI) 5 ptrichocarpa_eg_gene Populus trichocarpa genes (2004-12-JGI) 6 vvinifera_eg_gene Vitis vinifera genes (2007-12-IGGP) 7 athaliana_eg_gene Arabidopsis thaliana genes (TAIR9) ... > arabdset<-useMart(biomart="plant_mart_3", dataset = "athaliana_eg_gene") Checking attributes ... ok Checking filters ... ok > TSSArabAnno<-getAnnotation(arabdset, featureType="TSS") Error: segfault from C stack overflow > sessionInfo() R version 2.11.0 Under development (unstable) (2010-02-06 r51106) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.3.0 org.Hs.eg.db_2.3.6 [3] GO.db_2.3.5 RSQLite_0.8-2 [5] DBI_0.2-5 AnnotationDbi_1.9.4 [7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.15.4 [9] Biostrings_2.15.20 IRanges_1.5.40 [11] multtest_2.3.0 Biobase_2.7.4 [13] biomaRt_2.3.1 loaded via a namespace (and not attached): [1] MASS_7.3-5 RCurl_1.3-1 splines_2.11.0 survival_2.35-8 [5] tools_2.11.0 XML_2.6-0 > Thanks, P. Terry [email protected] [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
