Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
cannot estimate transcript abundances in Stringtie atonidas RNA Sequencing 1 05-26-2017 02:09 AM
stringtie output has exons instead of transcript annotation liux Bioinformatics 1 07-09-2015 05:39 AM
Tuxedo Pipeline Issue - Multiple Gene Hits per Transcript, High FPKM chimb Bioinformatics 1 08-07-2014 01:04 AM
Tuxedo Pipeline Issue - Multiple Gene Hits per Transcript, High FPKM chimb RNA Sequencing 0 08-06-2014 07:58 PM
aberrant FPKM for small transcript in Cufflinks (RABT mode) Nicolas Bioinformatics 0 11-30-2011 12:57 PM

Thread Tools
Old 05-31-2017, 01:43 AM   #1
Junior Member
Location: Germany

Join Date: Mar 2017
Posts: 1
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!
nachtwuenscher is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 11:27 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO