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Old 10-18-2011, 04:00 AM   #1
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Location: boston

Join Date: Oct 2011
Posts: 7
Default cufflinks


i'm getting Read type 0bp singled-end in the output of cufflinks, even it is 75bp. And, In the gene.fpkm/isoform file, it has lots of zero counts.

HTML Code:
$ cufflinks  -o /cufflinks/  -p 4 -g   /mm9    accepted_hits.sam
You are using Cufflinks v1.1.0, which is the most recent release.
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File accepted_hits.sam doesn't appear to be a valid BAM file, trying SAM...
[15:21:02] Loading reference annotation.
[15:21:04] Inspecting reads and determining fragment length distribution.
> Processed 29955 loci.                        [*************************] 100%
> Map Properties:
>	Total Map Mass: 20845338.50
>	#####NOTE HERE##### ====>>> Read Type: 0bp single-end
>	Fragment Length Distribution: Truncated Gaussian (default)
>	              Default Mean: 200
>	           Default Std Dev: 80
[15:23:56] Assembling transcripts and estimating abundances.
> Waiting for 2 threads to complete.           [************************ ]  99%
> Waiting for 1 threads to complete.           [************************ ]  99%
> Processed 29955 loci.                        [*************************] 100%
anyone who has got this before?

Last edited by victoryhe; 10-18-2011 at 04:02 AM.
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Old 01-31-2012, 07:57 AM   #2
Location: Granada, Spain

Join Date: Dec 2009
Posts: 12

Why don't you try using the BAM file instead of the SAM one?
mmanrique is offline   Reply With Quote

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