Wang, Xue, Ph.D.
2015-Sep-11 19:35 UTC
[R] the functionality of outputing junction reads in Rsubread package
Hi Rsubread developers and R users, I am using R version 3.1 and the associated "Rsubread" Bioconductor package. The "subjunc" function allows the user to output junction reads in the following format, #Chr, StartLeftBlock, EndRightBlock, Junction_Name, nSupport, Strand, StartLeftBlock, EndRightBlock, Color, nBlocks, BlockSizes, BlockStarts chr10 94009 94602 JUNC00000001 251 + 94009 94602 255,0,0 2 46,47 0,546 chr10 94822 95396 JUNC00000002 993 - 94822 95396 0,255,255 2 30,49 0,525 My question is, for the second last column (BlockSizes column), is there a way to modify the default maximum block size from 49 to other value (e.g. 20)? I understand this may involve the modification of source C code and re-compilation. Thanks, Xue
Jeff Newmiller
2015-Sep-11 21:12 UTC
[R] the functionality of outputing junction reads in Rsubread package
This belongs in an email to the Rsubread maintainers, e.g.
maintainer("Rsubread"), or on the Bioconductor mailing list.
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Sent from my phone. Please excuse my brevity.
On September 11, 2015 12:35:46 PM PDT, "Wang, Xue, Ph.D." <Wang.Xue
at mayo.edu> wrote:>Hi Rsubread developers and R users,
>
>I am using R version 3.1 and the associated "Rsubread"
Bioconductor
>package. The "subjunc" function allows the user to output junction
>reads in the following format,
>
>#Chr, StartLeftBlock, EndRightBlock, Junction_Name, nSupport, Strand,
>StartLeftBlock, EndRightBlock, Color, nBlocks, BlockSizes, BlockStarts
>chr10 94009 94602 JUNC00000001 251 + 94009 94602 255,0,0 2 46,47 0,546
>chr10
> 94822 95396 JUNC00000002 993 - 94822 95396 0,255,255 2 30,49 0,525
>
>My question is, for the second last column (BlockSizes column), is
>there a way to modify the default maximum block size from 49 to other
>value (e.g. 20)? I understand this may involve the modification of
>source C code and re-compilation.
>
>
>Thanks,
>
>
>Xue
>
>
>______________________________________________
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>and provide commented, minimal, self-contained, reproducible code.