[BioC] Interpretation of output files

from a TSSi user [guest] guest at bioconductor.org
Sat Aug 3 08:18:29 CEST 2013

I was able to successfully run TSSi program. However, I have several questions.

My questions are
- how "0.CUFF.16.1_2" is related to "0.CUFF.20.1_4",
- how region is determined to each gene,
- how this file could be interpreted,
- and how nTss is determined?

Thank you again for sparing your precious time.
Best regards.

 -- output of sessionInfo(): 

When I exported data by using the command bleow,

x <- segmentizeCounts(counts=counts, start=start, chr=chromosome, region=region, strand=strand)
yFit <- normalizeCounts( x, fit=TRUE )
z <- identifyStartSites( yFit )
segmentsRd <- segmentsAsRangedData( z )
export.gff3( segmentsRd, paste(tmpFile, "gff", sep=".") )

I could see some features corresponding to each gene.
s0_+_0.CUFF.16.1_2 rtracklayer sequence_feature 85285 87682 . - . chr=s0;region=0.CUFF.20.1_4;nPos=12;nCounts=860;nTss=11

Actually, according to annotation file, 0.CUFF.16.1_2 has starting site at 48426, whereas 0.CUFF.20.1_4 has starting site at 85285.

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