Hi All,
I have imported htseq-count data using the DESeqDataSetFromHTSeqCount function in DESeq2, and for a test I wanted to generate FPKMs from the count data.
However, that requires rowRanges, and that attribute is present but has no content. The htseq-count data just has gene names and counts, I clearly need to use the GTF to add the ranges.
I have looked literally half the day for some example of actually adding the rowRanges - the tutorial examples for DeSeq2 used canned examples with the ranges already there, I can't find any examples of how to do it from scratch.
I can figure out how to add it, but surely for something so basic there is a function already available somewhere.
Thanks!
Randy
I have imported htseq-count data using the DESeqDataSetFromHTSeqCount function in DESeq2, and for a test I wanted to generate FPKMs from the count data.
However, that requires rowRanges, and that attribute is present but has no content. The htseq-count data just has gene names and counts, I clearly need to use the GTF to add the ranges.
I have looked literally half the day for some example of actually adding the rowRanges - the tutorial examples for DeSeq2 used canned examples with the ranges already there, I can't find any examples of how to do it from scratch.
I can figure out how to add it, but surely for something so basic there is a function already available somewhere.
Thanks!
Randy
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