[BioC] Interpretation of output files

Julian Gehring julian.gehring at embl.de
Mon Aug 5 10:29:36 CEST 2013

Dear Soyeon Cha,

When you split the counts into segments (as you did by calling 
'segmentizeCounts'), each counts gets a name assigned.  By default, 
these names have the format '<chromosome>_<strand>_<region>, but you can 
change it with the 'pattern' argument in 'segmentizeCounts'.  As an 
example, 's0_+_0.CUFF.16.1_2' would be chromosome 's0', '+' strand, and 
region '0.CUFF.16.1_2'.

How this relates to the genes in your organism depends on the regions 
that you defined initially.  But since you have the coordinates of each 
start site, this should be easy to map back, even if you can't infer it 
from the region/segment name.

'nTSS' counts the number of identified start sites in each segment, as 
you also can see by inspecting 'z' with 'show'.

Best wishes

On 08/03/2013 08:18 AM, from a TSSi user [guest] wrote:
> Hello,
> 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.
> --
> Sent via the guest posting facility at bioconductor.org.
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