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NGS read summarization question


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#1 KPDE

KPDE

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Posted 12 September 2013 - 11:47 AM

What's a good way to do read summarization with equally sized bins as features? The output I am looking for is a count table that can be used for EdgeR (rows are genome features/bins and columns are feature name and integer count of reads within the named feature).

 

I've looked at F-seq and Hotspot but both work only in Linux which I'm unfamiliar with (i know, I know). The packages I know of in R require a GTF file to define the features for summarization but all I find for GTF files define features like exons, introns, etc. In addition, the programs I've seen for generating GTF files all use pre-existing feature files like BED which are also focused on genome features like introns, exons, etc. Is there a way to get or make GTF files that have selectably sized bins as features?

 

Thanks for any help,

 

NGS Neophyte


Edited by KPDE, 12 September 2013 - 01:37 PM.





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