cuffdiff single end reads

[madsaan]

hello,

am running cuffdiff between two single end reads and even thought it runs fine am getting a message as follows:

using default gaussian distribution due to insufficient paired-end reads in open ranges.it is recommended that correct parameters be provided(frag-len-mean and frag-len-std-dev)

when they say fragment length ,do they mean average read length?

thanks,
joji

[edge]

Hi madsaan,

Do you fix the problem already?
I'm facing the same error message as well
need your advice....

[madsaan]

hello edge,

I initially thought fragment length meant read length.Mine was 84 bp and I gave that as read length and i ended up without the warning message but my results were the same.When I later searched for it in seqanswers forum I found that frag-len-mean refers to the total sequence length (actual read + the adapter used during making the library). Also,if you use the version 0.9.3 you will not get the warning.
Hope this helps

[edge]

hi madsaan,

Thanks for reply.
I'm using the latest version of Cufflink 1.0.1 and run the following command"

Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks -p 4 -G Homo_sapiens.GRCh37.62.gtf --library-type fr-unstranded tophat_out/accepted_hits.bam 
Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks: /lib64/libz.so.1: no version information available (required by Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks)
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
[19:26:23] Loading reference annotation.
[19:26:37] Inspecting reads and determining fragment length distribution.
Processed 33455 loci.                        [*************************] 100%
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: 77344272.10
       Read Type: [B]0bp single-end[/B]
       Fragment Length Distribution: Truncated Gaussian (default)
                     Default Mean: 200
                  Default Std Dev: 80
[19:32:30] Estimating transcript abundances.
Processed 33455 loci.                        [*************************] 100%

My input file is 2X50bp, paired-end read.
I'm not sure why Cufflink will detect it as "0bp single-end".
Do you have any idea regarding the above error message?
If I'm using the "-g" option, the progress worked fine but the result is the same as the default Cufflink (without -g and Homo_sapiens.GRCh37.62.gtf in the command) running result

Cufflink/cufflinks-1.0.1.Linux_x86_64/cufflinks -p 4 -g Homo_sapiens.GRCh37.62.gtf --library-type fr-unstranded tophat_out/accepted_hits.bam

I was thinking just to assemble back the annotate transcript in my sample.
Thanks for any advice to improve the progress.

[clariet]

Edge, I am having the same error message. My dataset is 32bp single end. But cuffdiff gave the following message:

> Map Properties:
> Total Map Mass: 8533100.77
> Read Type: 0bp single-end
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80

I still got all those outputs. Did you figure out what the problem is? I would appreciate it very much if you or anyone else share your insights.

Clariet

[hrajasim]

Any resolution on this issue yet?
I still see "Read Type: 0bp single-end" in my cufflinks1.1.0 output.

[pinin4fjords]

me too

Edit: apologies for hasty posting- it was cuffmerge that was producing this message, not cuffdiff, which in fact displays more more sensible output (not sure why cuffmerge displays this though...).

I'm also experiencing this problem with 1.1.0. The relevant lines:

16:19:28] Inspecting reads and determining fragment length distribution.
Processed 28835 loci.                       
 Map Properties:
	Total Map Mass: 731211.00
	Read Type: 0bp single-end
	Fragment Length Distribution: Truncated Gaussian (default)
	              Default Mean: 200
	           Default Std Dev: 80

I'm using Illumana GAII 78 bp paired end so it doesn't make a lot of sense. I'm trying to determine if it impacts on the result.

[jp.]

anybody got solution ?