Hi all,
I've experienced a similar problem: I used Cufflinks 2.0.0 with the aim of fixing the problem of too many FAIL results (~30%) derived by the version 1.3.0. The results was that roughly one hundred transcripts were DE and all the others had zero values. As reported in the webpage of Cufflinks from the release 2.0.1 this problem should have been fixed . So I launched the last version 2.0.2 retrieving the same results of the 2.0.0: only 134 transcripts DE and all other with zero FPKM. From my personal experience the 1.0.3 is the last release that not gives strange results (although it gives a lot of false positive). Since them all subsequent releases that were supposed to give improvements miserly FAIL :-)
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by SeekRNA View PostI'm using cufflinks to compare expression in two conditions from modEncode BAM files. The FPKM values for both sets are zeros for every gene! There do not appear to be any errors (all are OK). What sorts of things give rise to this?
Thank you so much, and apologies if this is trivial as I am new to RNAseq
Leave a comment:
-
I had a similar problem when using v.2.0. Going back to a previous version helped. Although since that time I have discovered different problems with my original data (it was improperly filtered) thus it is possible that my cufflinks problem was due to the data and not the cufflinks version. Never-the-less if you are running v.2 then you may wish to try a different version.
Leave a comment:
-
Cufflinks giving all 0's
I'm using cufflinks to compare expression in two conditions from modEncode BAM files. The FPKM values for both sets are zeros for every gene! There do not appear to be any errors (all are OK). What sorts of things give rise to this?
Thank you so much, and apologies if this is trivial as I am new to RNAseq
Latest Articles
Collapse
-
by seqadmin
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...-
Channel: Articles
09-23-2024, 06:35 AM -
-
by seqadmin
During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.
Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...-
Channel: Articles
09-09-2024, 10:59 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 10-02-2024, 04:51 AM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
10-02-2024, 04:51 AM
|
||
Started by seqadmin, 10-01-2024, 07:10 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
10-01-2024, 07:10 AM
|
||
Started by seqadmin, 09-30-2024, 08:33 AM
|
0 responses
25 views
0 likes
|
Last Post
by seqadmin
09-30-2024, 08:33 AM
|
||
Started by seqadmin, 09-26-2024, 12:57 PM
|
0 responses
18 views
0 likes
|
Last Post
by seqadmin
09-26-2024, 12:57 PM
|
Leave a comment: