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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.
anyone who has got this before?
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.
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$ 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%
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