[R] the functionality of outputing junction reads in Rsubread package

Wang, Xue, Ph.D. Wang.Xue at mayo.edu
Fri Sep 11 21:35:46 CEST 2015

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.



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