Stringtie is breaking up an annotated gene

iriet · 04-08-2016, 11:52 AM

Hi,

I'm pretty new to RNA-seq analysis. I was able to map RNA-seq data with HISAT2, and am now trying to use Stringtie for the FPKM quantitations. I noticed that for some of the genes, Stringtie annotated the features as separate, presumably because there are no reads connecting the islands of mappings (even though my biological intuition would indicate they should be part of the same gene).

This is my invocation :
stringtie /SRR1818195.sorted.uniqmap.bam -p 8 -A gene_abund.tab -G knownGene.gtf -o SRR1818195.gtf

Below is an example of the type of result I would like to avoid (that these 3 separate features should be collapsed to one gene feature).

Thanks for any help!

##############################
Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM
STRG.11695 - 4 . 132107575 132109296 2.850755 3.370606 11.637426
STRG.11696 - 4 . 132109354 132109728 3.141333 3.702654 12.783860
STRG.11697 - 4 . 132113585 132113995 2.798054 3.303258 11.404900

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04-08-2016, 11:52 AM	#1
iriet Junior Member Location: New York Join Date: Nov 2015 Posts: 1	Stringtie is breaking up an annotated gene Hi, I'm pretty new to RNA-seq analysis. I was able to map RNA-seq data with HISAT2, and am now trying to use Stringtie for the FPKM quantitations. I noticed that for some of the genes, Stringtie annotated the features as separate, presumably because there are no reads connecting the islands of mappings (even though my biological intuition would indicate they should be part of the same gene). This is my invocation : stringtie /SRR1818195.sorted.uniqmap.bam -p 8 -A gene_abund.tab -G knownGene.gtf -o SRR1818195.gtf Below is an example of the type of result I would like to avoid (that these 3 separate features should be collapsed to one gene feature). Thanks for any help! ############################## Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM STRG.11695 - 4 . 132107575 132109296 2.850755 3.370606 11.637426 STRG.11696 - 4 . 132109354 132109728 3.141333 3.702654 12.783860 STRG.11697 - 4 . 132113585 132113995 2.798054 3.303258 11.404900