I have ben trying to run Htseq-count for quite a while now. Its containing throwing error as follows, Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/) Error occurred when reading the beginning of SAM/BAM file. No module named pysam
And so as it is mentioned I have installed pysam and when I run Htseq-count it still complains as No module named pysam I have installed pysam using pip install command line and as well as downloading the file. When I insatll pysam using pip its show as it is there Requirement already satisfied (use --upgrade to upgrade): pysam in /home/user/Tools/anaconda3/lib/python3.4/site-packages/pysam-0.9.0-py3.4-linux-x86_64.egg
However, I think the htseq-count doesn't consider anaconda version of pysam. And so as I think its not taking into account the downloaded and installed pysam package also.
Any suggestions would be great on this issue