derfinder and BAM indexes
2
0
Entering edit mode
@jessicahekman-6877
Last seen 9.2 years ago
United States

Hi all. I'm trying to get derfinder working. I have some pretty simple code right now:

 

library(derfinder)
library(Rsamtools)
b1 <- BamFile("tophat/tophat-juncs-10_130/accepted_hits.bam", index="tophat/tophat-juncs-10_130/accepted_hits.bam.bai")
fullCov <- fullCoverage(bl)

When I run this (R 3.1.1, updated Bioconductor yesterday), I get the error:

Error in loadCoverage(files = files, chr = chrs[idx], cutoff = NULL, bai = bai, : Not all BAM files have a BAM index. If the BAM index files are in a separate directory from the BAM files or are not named as 'bamFile.bam.bai' then consider using the 'bai' argument.

The BAI file does exist and I even specified it in the BamFile() call, so I'm not sure what's going on!

 

Thanks,

Jessica

derfinder • 2.1k views
ADD COMMENT
0
Entering edit mode
@lcolladotor
Last seen 16 days ago
United States

Hi Jessica,

`fullCoverage()` and `loadCoverage()` can take as input a character vector or a BamFileList object for the `files` argument, not a BamFile object. Your example however lead me to find a small bug when you input a BamFileList. In the meantime, use the functionality where you provide a character vector.

(Edit: BamFile and BigWigFile objects are now supported in `derfinder` versions 1.0.3 and 1.1.3 for release and devel respectively.)

That is, the equivalent of:

> library('derfinder')
> bam <- system.file('extdata', 'genomeData', 'ERR009101_accepted_hits.bam', package = 'derfinder')
> fullCov <- fullCoverage(bam, chrs = '21')
2014-10-16 16:22:24 fullCoverage: processing chromosome 21
2014-10-16 16:22:24 loadCoverage: finding chromosome lengths
2014-10-16 16:22:24 loadCoverage: loading BAM file /Library/Frameworks/R.framework/Versions/3.1/Resources/library/derfinder/extdata/genomeData/ERR009101_accepted_hits.bam
2014-10-16 16:22:24 loadCoverage: applying the cutoff to the merged data
2014-10-16 16:22:24 filterData: originally there were 48129895 rows, now there are 48129895 rows. Meaning that 0 percent was filtered.
> devtools::session_info()
Session info-----------------------------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.1.1 (2014-07-10)
 system   x86_64, darwin10.8.0        
 ui       AQUA                        
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/New_York            

Packages---------------------------------------------------------------------------------------------------------------------------------------
 package           * version  date       source        
 acepack             1.3.3.3  2013-05-03 CRAN (R 3.1.0)
 AnnotationDbi       1.28.0   2014-10-14 Bioconductor  
 base64enc           0.1.2    2014-06-26 CRAN (R 3.1.0)
 BatchJobs           1.4      2014-09-24 CRAN (R 3.1.1)
 BBmisc              1.7      2014-06-21 CRAN (R 3.1.0)
 Biobase             2.26.0   2014-10-14 Bioconductor  
 BiocGenerics        0.12.0   2014-10-14 Bioconductor  
 BiocParallel        1.0.0    2014-10-15 Bioconductor  
 biomaRt             2.22.0   2014-10-14 Bioconductor  
 Biostrings          2.34.0   2014-10-14 Bioconductor  
 bitops              1.0.6    2013-08-17 CRAN (R 3.1.0)
 brew                1.0.6    2011-04-13 CRAN (R 3.1.0)
 bumphunter          1.6.0    2014-10-14 Bioconductor  
 checkmate           1.4      2014-09-03 CRAN (R 3.1.1)
 cluster             1.15.3   2014-09-04 CRAN (R 3.1.1)
 codetools           0.2.9    2014-08-21 CRAN (R 3.1.1)
 DBI                 0.3.1    2014-09-24 CRAN (R 3.1.1)
 derfinder         * 1.1.2    2014-10-14 Bioconductor  
 derfinderHelper     1.0.1    2014-10-15 Bioconductor  
 devtools            1.6.1    2014-10-07 CRAN (R 3.1.1)
 digest              0.6.4    2013-12-03 CRAN (R 3.1.0)
 doRNG               1.6      2014-03-07 CRAN (R 3.1.1)
 fail                1.2      2013-09-19 CRAN (R 3.1.0)
 foreach             1.4.2    2014-04-11 CRAN (R 3.1.0)
 foreign             0.8.61   2014-03-28 CRAN (R 3.1.0)
 Formula             1.1.2    2014-07-13 CRAN (R 3.1.1)
 GenomeInfoDb        1.2.0    2014-10-14 Bioconductor  
 GenomicAlignments   1.2.0    2014-10-14 Bioconductor  
 GenomicFeatures     1.18.0   2014-10-14 Bioconductor  
 GenomicFiles        1.2.0    2014-10-14 Bioconductor  
 GenomicRanges       1.18.1   2014-10-16 Bioconductor  
 Hmisc               3.14.5   2014-09-12 CRAN (R 3.1.1)
 IRanges             2.0.0    2014-10-14 Bioconductor  
 iterators           1.0.7    2014-04-11 CRAN (R 3.1.0)
 lattice             0.20.29  2014-04-04 CRAN (R 3.1.0)
 latticeExtra        0.6.26   2013-08-15 CRAN (R 3.1.0)
 locfit              1.5.9.1  2013-04-20 CRAN (R 3.1.0)
 Matrix              1.1.4    2014-06-15 CRAN (R 3.1.0)
 matrixStats         0.10.0   2014-06-08 CRAN (R 3.1.0)
 nnet                7.3.8    2014-03-28 CRAN (R 3.1.0)
 pkgmaker            0.22     2014-05-14 CRAN (R 3.1.0)
 qvalue              1.40.0   2014-10-14 Bioconductor  
 R.methodsS3         1.6.1    2014-01-05 CRAN (R 3.1.0)
 RColorBrewer        1.0.5    2011-06-17 CRAN (R 3.1.0)
 RCurl               1.95.4.3 2014-07-29 CRAN (R 3.1.1)
 registry            0.2      2012-01-24 CRAN (R 3.1.0)
 rngtools            1.2.4    2014-03-06 CRAN (R 3.1.0)
 rpart               4.1.8    2014-03-28 CRAN (R 3.1.0)
 Rsamtools           1.18.0   2014-10-14 Bioconductor  
 RSQLite             0.11.4   2013-05-26 CRAN (R 3.1.0)
 rstudioapi          0.1      2014-03-27 CRAN (R 3.1.0)
 rtracklayer         1.26.0   2014-10-14 Bioconductor  
 S4Vectors           0.4.0    2014-10-14 Bioconductor  
 sendmailR           1.2.1    2014-09-21 CRAN (R 3.1.1)
 stringr             0.6.2    2012-12-06 CRAN (R 3.1.0)
 survival            2.37.7   2014-01-22 CRAN (R 3.1.0)
 XML                 3.98.1.1 2013-06-20 CRAN (R 3.1.0)
 xtable              1.7.4    2014-09-12 CRAN (R 3.1.1)
 XVector             0.6.0    2014-10-14 Bioconductor  
 zlibbioc            1.12.0   2014-10-14 Bioconductor  

 

Cheers,
Leo

ADD COMMENT
0
Entering edit mode

`derfinder` versions 1.0.3 and 1.1.3 for release and devel respectively address the issue reported here.

ADD REPLY
0
Entering edit mode
@jessicahekman-6877
Last seen 9.2 years ago
United States

Perfect -- I tried a character vector and it worked great. Thanks for your fast answer!

 

Jessica

ADD COMMENT
0
Entering edit mode

No problem! Fixes are completed. Details here.

ADD REPLY
0
Entering edit mode

Jessica, I believe that for the BioC support site to work properly you have to `accept` the answer. Otherwise it seems like no one has answered it.

Thanks,
Leo

ADD REPLY
0
Entering edit mode

Jessica, please select my answer as the answer to the question to close this thread.  To do so, just scroll up to my answer and click on "Accept!".

Thank you!

ADD REPLY

Login before adding your answer.

Traffic: 928 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6