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Simon-Leonard / APERO

small RNA detection from paired-end RNA-seq data
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APERO_end_detection output #5

Closed KKotryna closed 4 years ago

KKotryna commented 4 years ago

Hi, I wanted to ask about APERO_end_detection output. As I understand it should be a table containing start and end positions for each sRNA. I ran APERO with example BAM file and example script. The colnames of my results variables are: 

colnames(res2)
[1] "ID_Transcrit"           "Position"               "Positional.Uncertainty"
 [4] "lg"                     "str"                    "freq"                  
 [7] "iteration_nb"           "last_Ftsse"             "Class"                 
[10] "Comment"

Could you please provide more details/explanations about each column and its meaning?

Simon-Leonard commented 4 years ago

Hi,

Here is a description of each column : ID_Transcrit : Detected transcript ID Position : Start position of the detected transcript Positional.Uncertainty : Uncerntainty of the detected position (in nt) lg : Length of the detected RNA str : Strand of the detected RNA freq : Number of reads at the start positions iteration_nb : Number of iterations used to detect the RNA end (See the end detection method in APERO paper) last_Ftsse : Laste Ftsse value (see the APERO paper for the definition of Ftsse) Class : Annotation of the detected RNA according to supplementary figure 2 in APERO paper Comment : Detailed annotation

I will add this to the read me !

Bests, Simon