Hi I am NOT sure why running cufflinks failed here. Thanks for your suggestion,


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.