SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Problems with cuffmerge Nnogueira Bioinformatics 23 06-25-2016 09:38 PM
cuffmerge failed wall_y Bioinformatics 4 07-12-2012 06:25 AM
cuffmerge problem camelbbs RNA Sequencing 0 11-06-2011 04:58 PM
cuffmerge fail papori Bioinformatics 0 07-31-2011 03:01 PM
The test for cuffmerge fgh1124 Bioinformatics 5 07-28-2011 01:45 AM

Reply
 
Thread Tools
Old 10-04-2011, 12:46 AM   #1
Jolin
Member
 
Location: China

Join Date: Oct 2011
Posts: 10
Default Questions about cuffmerge

Hi, everyone, this is my first post here. I'm really worried about the problem I met. Can you help me?
I ran Tophat using paired-end reads and got .bam files. And then I ran Cufflinks and got .gtf files. Next, I ran cuffmerge with these .gtf files. And I met some problems here. The command line is as follows:

cuffmerge -g UCSC_hg19_gene_annot.gtf -s hg19.fa GTF_list.txt

But accroding to the report shown below, my paired-end reads were considered as single-end reads. This is very strange. What can I do to solve this problem?

Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
> Total Map Mass: 167431.00
> Read Type: 21499bp single-end ???????????
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[22:49:44] Assembling transcripts and estimating abundances.
Jolin 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 04:25 PM.


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