[BioC] problems running DEXseq

[Simon Anders]

Hi Diya

On 29/06/13 01:32, Diya wrote:

> 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

Correct would be

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

Before, you need to install HTSeq, as explained at
http://www-huber.embl.de/users/anders/HTSeq/doc/install.html

As Wolfgang already pointed out, your use of 'sudo' is very strange. I 
wonder if you might be following some incorrect instructions.

   Simon