Rseqc_ Installation Issue

Question

[lnzzz]

Hello everybody,

I would to use geneBody_coverage.py from RSeQC software to get the read distribution along transcripts in my RNA-seq libraries. Basically, I would like to see if I have a 5' or 3' shortening of transcripts.

When I tried to run it, I get this error :

ImportError: dlopen(/Library/Python/2.7/site-packages/RSeQC-2.3.7-py2.7-macosx-10.8-intel.egg/csamtools.so, 2): Symbol not found: ___ks_insertsort_heap
Referenced from: /Library/Python/2.7/site-packages/RSeQC-2.3.7-py2.7-macosx-10.8-intel.egg/csamtools.so
Expected in: flat namespace
in /Library/Python/2.7/site-packages/RSeQC-2.3.7-py2.7-macosx-10.8-intel.egg/csamtools.so

I think I may have an installation issue but my informatic skills are too weak to know how to deal with this problem.

I will appreciate very much you help!!!

Thank you

Answer 1

[wangliguo78]

This issue is related to pysam module installation. Try to install pysam by yourself, then rerun RSeQC script.

Test if pysam was installed successfully, type:

python -c 'import pysam'

If any error message, this meas pysam was not installed properly.

[liaoshun930914]

Thanks for sharing, it solves my problem.

For freshman of python..... There is a small tips....

Before install a new version of 'pysam'

Remember deleting the older version in RSeQC folder.