cufflinks

[victoryhe]

Hi,

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.

$ 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?

[mmanrique]

Why don't you try using the BAM file instead of the SAM one?