Hi I am NOT sure why running cufflinks failed here. Thanks for your suggestion,
tao ----------------------- Tool: Cufflinks Name: Cufflinks on data 6 and data 26: assembled transcripts Created: Sep 01, 2011 Filesize: 81.3 Mb Dbkey: hg19 Format: gtf Tool Version: Input Parameter Value SAM or BAM file of aligned RNA-Seq reads 6: Tophat for R4_CG_wh_accepted_hits Max Intron Length 300000 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Aonnotation 26: Homo_sapiens.GRCh37.63.gtf Conditional (bias_correction) 0 Conditional (seq_source) 0 Conditional (singlePaired) 0 ---------------------------------------------------------- Message from History panel in GALAXY: An error occurred running this job: cufflinks v1.0.3 cufflinks -q --no-update-check -I 300000 -F 0.050000 -j 0.050000 -p 8 -N -b /galaxy/data/hg19/sam_index/hg19.fa Error running cufflinks. [18:40:45] Inspecting reads and determining fragment length distribution. Processed 915556 loci.
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