[Bioc-sig-seq] Annotation of ChIP-Seq peaks

[Muino, Jose]

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: bioc-sig-sequencing-bounces at r-project.org en nombre de pterry at huskers.unl.edu
Enviado el: lun 08/02/2010 15:59
Para: bioc-sig-sequencing at r-project.org
CC: pterry at huskers.unl.edu
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
pterry at huskers.unl.edu

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