Hello.
I used Cufflinks to process data from tophat.
My data come from Illumina and are pair-end type.
I type following command:
Unfortunately Cufflinks recognize that data as single-end and lenght 0!
Is it necesarry to use some more option to correct run Cufflinks on pair-end data?
I used Cufflinks to process data from tophat.
My data come from Illumina and are pair-end type.
I type following command:
Code:
/path/cufflinks tophat_out/accepted_hits.bam -o cuff_out
Unfortunately Cufflinks recognize that data as single-end and lenght 0!
Code:
[13:40:01] Inspecting reads and determining fragment length distribution. Processed 204293 loci. Map Properties: Total Map Mass: 5928337.99 [B]Read Type: 0bp single-end[/B] Fragment Length Distribution: Truncated Gaussian (default) Default Mean: 200 Default Std Dev: 80 [13:52:49] Assembling transcripts and estimating abundances. Processed 204293 loci.
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