Hi, I have a GAlignments object which I read from a bam file and have modified. I would like to write the modified GAlignments object now to a new bam file. I only came across the filterBam option in Rsamtools which I don't think will work. Is there any way to do this? If so, I would also like to be able to provide it with a header. -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] doParallel_1.0.3 iterators_1.0.6 foreach_1.4.1 data.table_1.8.10 Rsamtools_1.13.44 Biostrings_2.29.19 GenomicRanges_1.13.45 XVector_0.1.4 [9] IRanges_1.19.38 BiocGenerics_0.7.5 loaded via a namespace (and not attached): [1] bitops_1.0-6 codetools_0.2-8 stats4_3.0.2 tools_3.0.2 zlibbioc_1.7.0 -- Sent via the guest posting facility at bioconductor.org.

On 09/28/2013 12:44 PM, rubi [guest] wrote: > > Hi, > > I have a GAlignments object which I read from a bam file and have modified. I would like to write the modified GAlignments object now to a new bam file. I only came across the filterBam option in Rsamtools which I don't think will work. Is there any way to do this? > If so, I would also like to be able to provide it with a header. No, writing new or modified records is a big gap in the current Rsamtools; I know that the CRAN package rbamtools has write capabilities, but I have not used it and do not know how well / if it would play with Rsamtools (or perhaps its approach is sufficient for your purposes). Martin > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] doParallel_1.0.3 iterators_1.0.6 foreach_1.4.1 data.table_1.8.10 Rsamtools_1.13.44 Biostrings_2.29.19 GenomicRanges_1.13.45 XVector_0.1.4 > [9] IRanges_1.19.38 BiocGenerics_0.7.5 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 codetools_0.2-8 stats4_3.0.2 tools_3.0.2 zlibbioc_1.7.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793