Question: (Closed) Why Do Genome Features With Identical Coordinates Show Different Fpkm Values? (Tophat/Cufflinks)
1
gravatar for Liye Zhang
6.8 years ago by
Liye Zhang80
United States
Liye Zhang80 wrote:

Hi, all:

when I checked my paired-end RNAseq data, I saw some weird result. Figure is here

basically two genome features have same coordinate(as highlighted in red), however, their fpkm value is different. I wonder anyone have some ideas why this occur?

By the way, I am using Tophat v2.0.4, Cufflinks v2.0.2 and cummeRbund v2.0.0.

Thanks.

Best, Liye

fpkm rna-seq • 2.0k views
ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Liye Zhang80
0
gravatar for Istvan Albert
6.8 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

Well the genes that you list there are not supposed to have the same coordinates ... so this means there is some inconsistency there - one or more of the files is not what you think they are - or something else ...

ADD COMMENTlink written 6.8 years ago by Istvan Albert ♦♦ 80k
0
gravatar for Liye Zhang
6.8 years ago by
Liye Zhang80
United States
Liye Zhang80 wrote:

I check the annotation for DDX11L1 of chr1, which spans 11869 to 13670. And RP11-34P13.3 spans 29554 to 30039. And Has-mir-1302-2 starts from 30366 to 30503.

Therefore, I think the locus represents a transcript contig defined by cufflinks, which may include multiple transcripts. And each can have an unique ID. Therefore, both XLOC0001 and XLOC_00002 is within contig chr1:11868-31109. Therefore, it is possible that two transcripts within a contig have differential gene expression.

ADD COMMENTlink written 6.8 years ago by Liye Zhang80
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1559 users visited in the last hour