Hi, 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 file. 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. Thanks, Diya

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

Dear Diya it appears that you are running dexseq_count.py as if it were a shell script, rather than from Python. As a consequence, the first line of the script is interpreted as the Linux command 'import' rather than as Python code, leading to the error you report. It also seems a bit troubling that you run this code as a superuser. That should never be necessary. Maybe best would be for you to hook up locally with a sys admin or with someone knowledgeable in Unix scripting, since it seems difficult to diagnose your particular system architecture remotely. Best wishes Wolfgang On Jun 29, 2013, at 1:32 am, Diya <dvaka at="" stanford.edu=""> wrote: > Hi, > > 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 > file. > 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. > > Thanks, > > Diya > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Hi Diya, Please use "reply all" when responding to mails from this list so that discussion stays "on line" and is visible by more people. This way you will likely get better help, and we can also use these lists as a source of help for other people who are doing similar things. That having been said: > Thanks for your response and the PDF file.. It really helps. I have aligned fastq reads to UCSC hg 19 genome.in that case how can I use the genomic ranges for UCSC specific genome.. ? You would use a GenomicFeatures::TranscriptDb object built from gene annotations against hg19. This pre-compiled one would be a good place to start: http://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsa piens.UCSC.hg19.knownGene.html Which I believe was compiled from the UCSC knownGene table: https://genome.ucsc.edu/FAQ/FAQdownloads.html#download31 HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech