Dear List,

	I am working through the easyRNASeq use case.
(easyRNASeq: an overview Oct 16, 2012, section 7)
I am working on a Mac so I could not do the alignment
part of the use case but rather started with bam files
produced by top hat:


ccrfml1:learning_easyRNAseq friedman$ ls
490224.bam			easyRNAseqworkingscripts.txt
490225.bam			learningRNASeq.docx
easyRNASeqvignette2.txt

Here is my session record:

> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] easyRNASeq_1.4.2       ShortRead_1.16.2       latticeExtra_0.6-19    RColorBrewer_1.0-5    
 [5] lattice_0.20-10        Rsamtools_1.10.2       DESeq_1.10.1           locfit_1.5-8          
 [9] BSgenome_1.26.1        GenomicRanges_1.10.5   Biostrings_2.26.2      IRanges_1.16.4        
[13] edgeR_3.0.4            limma_3.12.1           biomaRt_2.14.0         Biobase_2.18.0        
[17] genomeIntervals_1.14.0 BiocGenerics_0.4.0     intervals_0.13.3      

loaded via a namespace (and not attached):
 [1] annotate_1.34.1      AnnotationDbi_1.20.2 bitops_1.0-4.1       DBI_0.2-5            genefilter_1.38.0   
 [6] geneplotter_1.34.0   grid_2.15.2          hwriter_1.3          RCurl_1.91-1         RSQLite_0.11.1      
[11] splines_2.15.2       stats4_2.15.2        survival_2.36-14     tools_2.15.2         XML_3.9-4          
[16] xtable_1.7-0         zlibbioc_1.2.0      


> chr.sizes=seqlengths(Hsapiens)
> chr.sizes
                 chr1                  chr2                  chr3                  chr4 
            249250621             243199373             198022430             191154276 
                 chr5                  chr6                  chr7                  chr8 
            180915260             171115067             159138663             146364022 
                 chr9                 chr10                 chr11                 chr12 
            141213431             135534747             135006516             133851895 
                chr13                 chr14                 chr15                 chr16 
            115169878             107349540             102531392              90354753 
                chr17                 chr18                 chr19                 chr20 
             81195210              78077248              59128983              63025520 
                chr21                 chr22                  chrX                  chrY 
             48129895              51304566             155270560              59373566 
                 chrM  chr1_gl000191_random  chr1_gl000192_random        chr4_ctg9_hap1 
                16571                106433                547496                590426 
 chr4_gl000193_random  chr4_gl000194_random         chr6_apd_hap1         chr6_cox_hap2 
               189789                191469               4622290               4795371 
        chr6_dbb_hap3        chr6_mann_hap4         chr6_mcf_hap5         chr6_qbl_hap6 
              4610396               4683263               4833398               4611984 
       chr6_ssto_hap7  chr7_gl000195_random  chr8_gl000196_random  chr8_gl000197_random 
              4928567                182896                 38914                 37175 
 chr9_gl000198_random  chr9_gl000199_random  chr9_gl000200_random  chr9_gl000201_random 
                90085                169874                187035                 36148 
chr11_gl000202_random       chr17_ctg5_hap1 chr17_gl000203_random chr17_gl000204_random 
                40103               1680828                 37498                 81310 
chr17_gl000205_random chr17_gl000206_random chr18_gl000207_random chr19_gl000208_random 
               174588                 41001                  4262                 92689 
chr19_gl000209_random chr21_gl000210_random        chrUn_gl000211        chrUn_gl000212 
               159169                 27682                166566                186858 
       chrUn_gl000213        chrUn_gl000214        chrUn_gl000215        chrUn_gl000216 
               164239                137718                172545                172294 
       chrUn_gl000217        chrUn_gl000218        chrUn_gl000219        chrUn_gl000220 
               172149                161147                179198                161802 
       chrUn_gl000221        chrUn_gl000222        chrUn_gl000223        chrUn_gl000224 
               155397                186861                180455                179693 
       chrUn_gl000225        chrUn_gl000226        chrUn_gl000227        chrUn_gl000228 
               211173                 15008                128374                129120 
       chrUn_gl000229        chrUn_gl000230        chrUn_gl000231        chrUn_gl000232 
                19913                 43691                 27386                 40652 
       chrUn_gl000233        chrUn_gl000234        chrUn_gl000235        chrUn_gl000236 
                45941                 40531                 34474                 41934 
       chrUn_gl000237        chrUn_gl000238        chrUn_gl000239        chrUn_gl000240 
                45867                 39939                 33824                 41933 
       chrUn_gl000241        chrUn_gl000242        chrUn_gl000243        chrUn_gl000244 
                42152                 43523                 43341                 39929 
       chrUn_gl000245        chrUn_gl000246        chrUn_gl000247        chrUn_gl000248 
                36651                 38154                 36422                 39786 
       chrUn_gl000249 
                38502 

>  bamfiles=dir(getwd(),pattern="*\\.bam$")
> bamfiles
[1] "490224.bam" "490225.bam"
> rnaSeq <- easyRNASeq(filesDirectory=getwd(),
+                      organism="Hsapiens",
+                      chr.sizes=chr.sizes,
+                      readLength=58L,
+                      annotationMethod="biomaRt",
+                      count="exons",
+                      filenames=bamfiles[1],
+                      outputFormat="RNAseq"
+                      )
Checking arguments... 
Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes,  : 
  You must indicate the format of you source files, by setting argument 'format'

COMMENT: I THOUGHT THAT BAM FILES WERE AUTOMATICALLY THE INPUT
FILE FORMAT,

> rnaSeq <- easyRNASeq(filesDirectory=getwd(),
+                      organism="Hsapiens",
+                      chr.sizes=chr.sizes,
+                      readLength=58L,
+                      annotationMethod="biomaRt",
+                      count="exons",
+ 		     format="bam",
+                      filenames=bamfiles[1],
+                      outputFormat="RNAseq"
+                      )
Checking arguments... 
Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes,  : 
  Index files (bai) are required. They are missing for the files: /Documents/clients/Phyllis/learning_easyRNAseq/490224.bam

QUESTION: HOW DI I OBTAIN OR PRODUCE THESE INPUT FILES?

Thanks and best wishes,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

In memoriam, Ray Bradbury


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