Thanks for the previous help in using derfinder! At this point my code looks like this:

source("http://bioconductor.org/biocLite.R")
biocLite("derfinder")
library(derfinder)
fullCov1 <- fullCoverage(c("tophat/tophat-juncs-10_130/accepted_hits.bam"), chrs="1")

However, the object returned by fullCoverage shows 0 hits at every nucleotide position (I used summary() to check). I also tried loading a different chromosome instead of 1, and got an error for the 3 of them that I checked:

> fullCov2 <- fullCoverage(c("tophat/tophat-juncs-10_130/accepted_hits.bam"), chrs="2")
2014-10-20 16:02:37 fullCoverage: processing chromosome 2
2014-10-20 16:02:38 loadCoverage: finding chromosome lengths
Error: 1 errors; first error:
  Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges"): solving row 2: range cannot be determined from the supplied arguments (too many NAs)

My BAM files do have alignments in them, so I'm not sure what's going on or how to debug this problem. I'd appreciate insights!

Thanks,

Jessica

Hello,

Here is the full answer to this question.

During the interchange of comments, we realized two things. First, `summary()` was being used on the first row of one sample (which will frequently be all 0s) instead of all the bases in a chromosome from one sample. Second, `derfinder` relies on `GenomeInfoDb` for using the correct sequence naming style. The interaction with `GenomeInfoDb` was too rigid and `derfinder` broke when analyzing data from an organism not present in `GenomeInfoDb`.

After quite a bit of work, version 1.1.5 of `derfinder` (Bioc-devel) and 1.0.4 (Bioc-release) have fixed this issue as can be seen below.

First we load `derfinder`, specify the BAM file, and load the coverage data for all _Canis familiaris_ chromosomes.

> library('derfinder')
## BAM file: http://arborius.net/~jphekman/10_130-chr11.bam
## BAI file: http://arborius.net/~jphekman/10_130-chr11.bam.bai
> bam <- '10_130-chr11.bam'
> fullCov <- fullCoverage(bam, chrs = c(1:38, 'MT', 'X'),
+     species = 'canis_familiaris')
## Lots of messages deleted
## species = 'canis_familiaris' is at this moment not supported by GenomeInfoDb but should be soon
## given https://support.bioconductor.org/p/62136/#62180
## In any case, derfinder doesn't crash.

Next we can verify that there is only coverage information for chromosome 11 because that is the way the BAM file was constructed.

## Check that there is some coverage info for the first sample
## Given how the BAM file was constructed, there will only be data for chr 11.
> sapply(fullCov, function(x) { sum(x[[1]])})
       1        2        3        4        5 
       0        0        0        0        0 
       6        7        8        9       10 
       0        0        0        0        0 
      11       12       13       14       15 
39961057        0        0        0        0 
      16       17       18       19       20 
       0        0        0        0        0 
      21       22       23       24       25 
       0        0        0        0        0 
      26       27       28       29       30 
       0        0        0        0        0 
      31       32       33       34       35 
       0        0        0        0        0 
      36       37       38       MT        X 
       0        0        0        0        0 
       

Below is the correct `summary()` call and an illustration of the dimensions of the data.
       
## Dimension per chr is number of base pairs in chr times number of samples
> dim(fullCov[[1]])
[1] 122678785         1 

## Correct summary() call for the first sample in chr11
> summary(fullCov[['11']][[1]])
    Min.  1st Qu.   Median     Mean  3rd Qu. 
   0.000    0.000    0.000    0.537    0.000 
    Max. 
7799.000 

Reproducibility information.
      
## Versions used
> packageVersion('derfinder')
[1] ‘1.1.5’
> packageVersion('GenomeInfoDb')
[1] ‘1.2.0’

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Best,
Leo

PS Details here.