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Old 01-21-2015, 08:24 AM   #1
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Location: Münster, Germany

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Default Need help by quantifying overlapping reads with with the dRNA-Seq tool READemption

Hi everybody,

I'm a beginner in Ubuntu and i have just installed the program READemption, which is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples.
The installation was no problem but I'm now trying to perform an example analysis. an example analysis, which is given on the website (

I downloaded the reference sequences, the GFF3 files that contain the annotations and the reads of the reads RNA-Seq libraries.

The poly a clipping, which is done by typing in "reademption align -p 4 --poly_a_clipping READemption_analysis" was no problem. To generate the
coverage files by typing in "reademption coverage -p 4 READemption_analysis"
also worked.

I'm now trying to count the number of reads overlapping with each of the annotation entries by typing in
"reademption gene_quanti -p 4 --features CDS,tRNA,rRNA READemption_analysis"
which the given command in the example analysis.
Im using Ubuntu 14.10 and READemption 0.3.5. My Python version is 3.4.

I get the following error:

lars@lars-VirtualBox:~$ reademption gene_quanti -p 4 --features CDS,tRNA,rRNA READemption_analysis
Traceback (most recent call last):
File "/usr/local/bin/reademption", line 268, in <module>
File "/usr/local/bin/reademption", line 240, in main
File "/usr/local/bin/reademption", line 254, in run_gene_wise_quantification
File "/usr/local/lib/python3.4/dist-packages/reademptionlib/", line 607, in quantify_gene_wise
File "/usr/local/lib/python3.4/dist-packages/reademptionlib/", line 572, in _check_job_completeness
TypeError: overlap() takes no arguments (2 given)

Has anyone an idea why that error occurs ? Unfortunately, I can't fix the problem by myself.


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