I am running CIRIquant on UBUNTU 20.04 LTS following the guidelines indicated on https://ciriquant-cookbook.readthedocs.io/en/latest/de.html. After a successful circRNA quantification step, I run the Differential expression analysis with biological replicates. I also run the prepDE.py -i sample_gene.lst step successfully.
But while running prep_CIRIquant using
prep_CIRIquant -i sample.lst
--lib library_info.csv
--circ circRNA_info.csv
--bsj circRNA_bsj.csv
--ratio circRNA_ratio.csv
I get an IndexError message:
File "/home/mamu/miniconda3/envs/py2/lib/python2.7/site-packages/CIRIquant-1.1-py2.7.egg/CIRIquant/prep_CIRIquant.py", line 89, in main
sample, sample_file, group = content[0], content[1], content[2]
IndexError: list index out of range.
I tried to search on the net about the issue and I didn't find any solutions yet.
Can you please help me in solving this issue?
I would like to thank you all in advance for your help.
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I think it might be good to answer my own question here. With the support of the author of the tool, I found out that the error was created due to extra space present at the end of the
sample.lstfile. Thus, removing the extra spaces is the solution. Thank youJinyangfor your immediate response.