search

Simon-Leonard / APERO

small RNA detection from paired-end RNA-seq data
3 stars 5 forks source link

APERO end detection output #9

Closed anfarr closed 2 years ago

anfarr commented 2 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

Originally posted by @Simon-Leonard in https://github.com/Simon-Leonard/APERO/issues/5#issuecomment-632677901

Hey Simon, i have two questions. Shouldn't last_Ftsse be defined as "last Fstart,e" to make the connection to the paper? And is the coordinate of the position, 0 based like the bam file or 1-based? Best regards, Anton

Simon-Leonard commented 2 years ago

Hi,

That is correct, last_Ftsse corresponds to last Fstart,e. The coordinates are 1-based.

Simon