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Old 05-31-2017, 12:43 AM   #1
nachtwuenscher
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Location: Germany

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Default Zero FPKM value for transcript in Stringtie

I just analyzed a dataset of 49 samples and found a zero FPKM-value in 11 of these in my favourite gene (SOX2) using texpr()-data extraction. Looking at the exon wise read counts they show nearly exact the same median value as the samples that had FPKM values > 0 (i.e. rcount value of 7800, FPKM of 41, the transcript has only one exon).
What might have had happened?
SOX2 has only one isoform and consists of only a single exon in my annotation.
Thanks for your help!
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