[BioC] problems running DEXseq

Diya dvaka at stanford.edu
Sat Jun 29 01:32:24 CEST 2013


We want to explore DEXseq to see if we find anything interesting for alt-
splicing analysis. I have aligned the reads using iGenomes UCSC genome files 
for hg19 genome. We have 2 Control and 3 KD samples( biological replicates).

I have successfully passed the first step where in I prepapred the annotation 
The second step which is "for counting " I encounter errors. 

The command used is 
sudo samtools view ./Control_N1/Control_N1_thout/accepted_hits.sorted.bam | 
/data1/Bethsaida/python_scripts/dexseq_count.py -p yes 
HS.GRCh37.72_norm.DEXSeq.gff - combined.txt

Error message:

import: unable to open X server `' @ error/import.c/ImportImageCommand/366.
/data1/Bethsaida/python_scripts/dexseq_count.py: line 3: syntax error near 
unexpected token `('
/data1/Bethsaida/python_scripts/dexseq_count.py: line 3: `optParser = 
optparse.OptionParser( '

Any help, so that I can start running the next steps.



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