Hi,
I used hisat2 (2.0.5) to map 150b Paired-end reads on to the draft genome of castorbean and used cufflinks (version 2.2.1) to perform reference annotation based transcript assembly (RABT). This data is NOT for differential expression analysis. The assembler reported novel isoforms and some novel genes. From the results, of the transcripts that were as present in the gtf file used for RABT, some had an FPKM value of "0.0000000000" but were "yes" for "full_read_support" whereas the rest that were "yes" for "full_read_support" carried an FPKM value at 1 or above.
Could anyone please explain why would a transcript be described as present with "full_read_support," yet with an FPKM value of "0.0000000000?"
Thanks.
I used hisat2 (2.0.5) to map 150b Paired-end reads on to the draft genome of castorbean and used cufflinks (version 2.2.1) to perform reference annotation based transcript assembly (RABT). This data is NOT for differential expression analysis. The assembler reported novel isoforms and some novel genes. From the results, of the transcripts that were as present in the gtf file used for RABT, some had an FPKM value of "0.0000000000" but were "yes" for "full_read_support" whereas the rest that were "yes" for "full_read_support" carried an FPKM value at 1 or above.
Could anyone please explain why would a transcript be described as present with "full_read_support," yet with an FPKM value of "0.0000000000?"
Thanks.
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