Question: StringTie inconsistent expression value
gravatar for nand
11 days ago by
nand10 wrote:

I'm trying to find novel isoforms from RNA-Seq. I have six samples, 3 control and 3 treatment. I made a merged gtf file after running StringTie with gencode annotation. Then the merged annotation was used to estimate FPKM in all samples. Then novel transcripts expression was tabulated as shown below. The left three columns are control and the right three are treatment. Why is the fpkm absolute zero for in some cases, when it is very high for the same transcript in other samples.

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rna-seq • 69 views
ADD COMMENTlink modified 11 days ago by genomax43k • written 11 days ago by nand10

Have you loaded the BAM into IGV and gone into that locus to check? Most of the times, inspecting in IGV resolves doubt about differences in expression estimate (from assembler).

ADD REPLYlink written 11 days ago by Amitm1.4k

I loaded BAM and merged GTF to IGV. I am seeing many fragments aligned to that transcript region. But FPKM is absolutely zero.

ADD REPLYlink written 10 days ago by nand10
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