Question: Running Cufflinks
0
Peng, Tao • 170 wrote:
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.