Question: StringTie inconsistent expression value
0
gravatar for nand
9 months ago by
nand10
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.

enter image description here

rna-seq • 299 views
ADD COMMENTlink modified 9 months ago by genomax59k • written 9 months ago by nand10
1

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 9 months ago by Amitm1.6k

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 9 months ago by nand10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1162 users visited in the last hour