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Old 10-04-2011, 12:46 AM   #1
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.
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