SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffdiff output files are empty pinki999 Bioinformatics 1 05-21-2012 07:49 AM
CDS vs cDNA s13ep MGISEQ (FKA Complete Genomics) 4 04-20-2012 02:19 PM
cuffdiff replicates empty results fangquan Bioinformatics 7 09-07-2011 11:21 PM
How can I look up CDS from NCBI litc Bioinformatics 1 12-06-2010 01:03 PM
Empty cuffdiff files repinementer Bioinformatics 1 08-17-2010 09:57 PM

Reply
 
Thread Tools
Old 02-16-2011, 10:05 AM   #1
joseph
Member
 
Location: ca

Join Date: Feb 2008
Posts: 39
Default why cuffdiff cds-tests empty?

Hi

I ran cuffcompare with the reference annotation "refGene.gtf" which is RefSeq Genes (refGene) track from UCSC GB.
Code:
cuffcompare -V -r refGene.gtf -R -o s7_s8_refGene transcripts_s7.gtf transcripts_s8.gtf
I noticed that in the "*.combined.gtf" output there is an attribute oId instead of p_id:
Code:
chr1	Cufflinks	exon	4797909	4798063	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00001337"; exon_number "1"; oId "s_8.310184.1"; nearest_ref "NM_008866"; class_code "j"; tss_id "TSS1";
chr1	Cufflinks	exon	4798536	4798567	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00001337"; exon_number "2"; oId "s_8.310184.1"; nearest_ref "NM_008866"; class_code "j"; tss_id "TSS1";
When I ran cuffdiff, the "cds.diff" and "cds.fpkm_tracking" files came out empty:
Code:
cuffdiff -N -L s_7,s_8 -p 2 -v -r ~/mm9.fa s7_s8_refGene.combined.gtf accepted_hits_s7.bam accepted_hits_s8.bam

..........
Processed 18302 loci. Performed 4816 isoform-level transcription difference tests
Performed 574 tss-level transcription difference tests
Performed 2853 gene-level transcription difference tests
Performed 0 CDS-level transcription difference tests
Performed 203 splicing tests
Performed 131 promoter preference tests
Performing 0 relative CDS output tests
Writing isoform-level FPKM tracking
Writing TSS group-level FPKM tracking
Writing gene-level FPKM tracking
Writing CDS-level FPKM tracking
Any suggestions will be appreciated.
Thanks
joseph is offline   Reply With Quote
Old 02-17-2011, 06:25 AM   #2
honey
Senior Member
 
Location: Pittsburgh

Join Date: Feb 2010
Posts: 151
Default Cds

Assuming you are working with hg19- Use hg19.fa file and -s option while running cuffcompare
honey is offline   Reply With Quote
Old 02-17-2011, 10:33 AM   #3
joseph
Member
 
Location: ca

Join Date: Feb 2008
Posts: 39
Default cds

Quote:
Originally Posted by honey View Post
Assuming you are working with hg19- Use hg19.fa file and -s option while running cuffcompare
That solved the problem. Thank you for caring and answering my question.
Joseph
joseph is offline   Reply With Quote
Reply

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 04:37 PM.


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