SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq2: bad experimental design and "not full rank" problems Erinyes Bioinformatics 2 09-15-2015 01:40 AM
DESeq2 paired data: "model is not full rank" sbcn Bioinformatics 5 09-14-2015 11:03 AM
Bcl2Fastq 1.8.3 install error on Ubuntu 12.04LTS: "No support for bzip2 compression" slees Bioinformatics 3 10-26-2013 01:52 AM
How does cuffdiff/cufflinks determine "read type"? sdarko Bioinformatics 3 08-31-2011 11:13 PM
calibrated quality string "B" full Trudy Bioinformatics 2 03-25-2011 10:04 AM

Reply
 
Thread Tools
Old 04-21-2017, 09:05 PM   #1
velu
Junior Member
 
Location: Hyderabad, India

Join Date: Sep 2015
Posts: 4
Default with cufflinks, can there be "0" fpkm value and yet full read support?

Hi,
I used hisat2 (2.0.5) to map 150b Paired-end reads on to the draft genome of castorbean and used cufflinks (version 2.2.1) to perform reference annotation based transcript assembly (RABT). This data is NOT for differential expression analysis. The assembler reported novel isoforms and some novel genes. From the results, of the transcripts that were as present in the gtf file used for RABT, some had an FPKM value of "0.0000000000" but were "yes" for "full_read_support" whereas the rest that were "yes" for "full_read_support" carried an FPKM value at 1 or above.
Could anyone please explain why would a transcript be described as present with "full_read_support," yet with an FPKM value of "0.0000000000?"

Thanks.
velu is offline   Reply With Quote
Old 04-24-2017, 07:00 PM   #2
Dario1984
Senior Member
 
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166
Default

I have noticed similar problems with Cufflinks in the past. Our research group no longer uses it because it hasn't been updated in 3 years and some of the FPKM values look suspicious, which you have noticed.
Dario1984 is offline   Reply With Quote
Old 04-25-2017, 04:31 AM   #3
velu
Junior Member
 
Location: Hyderabad, India

Join Date: Sep 2015
Posts: 4
Default

Thank you, Dario1984.
Then, what method do you follow for the assembly of reads that do not have such limitations?
velu is offline   Reply With Quote
Old 04-25-2017, 06:00 PM   #4
Dario1984
Senior Member
 
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 166
Default

We use Trinity because we found its results can be experimentally validated by biologists. There's also a genome guided assembly mode. It was developed a few years ago, but it still maintained by the developer. You might also be interested in categorising your assembled transcripts with TransDecoder.
Dario1984 is offline   Reply With Quote
Old 04-25-2017, 06:23 PM   #5
velu
Junior Member
 
Location: Hyderabad, India

Join Date: Sep 2015
Posts: 4
Default

Thank you.
I will go through the possibilities you have suggested.
velu is offline   Reply With Quote
Reply

Tags
cufflinks 2.2.1, fpkm 0, full read support, rabt assembly

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 07:04 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO