Dario Strbenac | 11 Jan 02:00 2013
Picon

Re: BAM files to Genomic Ranges object

>That code looks correct, but I would rather do:
>
>   bam_files <- list.files(pattern="*.bam")
>   gr_list <- lapply(bam_files,
>                     function(bam_file)
>                       as(readGappedAlignments(bam_file), "GRanges"))
>   names(gr_list) <- bam_files

Is it possible to add an option to the coercion to keep the metadata columns ? For example, if the user
specifies they also want to read the quality scores, the coercion to GRanges currently discards that.

_______________________________________________
Bioconductor mailing list
Bioconductor@...
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


Gmane