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The probability of alternative transcript #404

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dudududu12138 opened this issue Jan 28, 2024 · 0 comments
Open

The probability of alternative transcript #404

dudududu12138 opened this issue Jan 28, 2024 · 0 comments

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@dudududu12138
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dudududu12138 commented Jan 28, 2024

Hello, I use Augustus to predict alternative transcripts. The result is in gff format. But I don't understand the 6th column. It looks like probabilities. But I noticed that the values of a gene is the sum of values of the transcripts. For example, transcripts g1.t1 and g1.t2 are 0.08 and 0.02 while gene g1 is 0.1. So what's the meaning of column 6? And do I need to filter the results according to column 6? If so, what's the proper threshold?
Here is my code:

singularity exec $augustus augustus --species=human \
        --alternatives-from-sampling=true \
        --sample=100 \
        --minexonintronprob=0.1 \
        --minmeanexonintronprob=0.4 \
        --maxtracks=-1 \
        chr21.fa >chr21.alt.gff

And the result is listed below:
ef249ae7e4dedcb9294216a7f1b3f1a

Thank you very much!

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