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cuffmerge script error

hello,

I am trying to use cuffmerge tool of cufflinks suite for differential analysis but it is showing error reports in python script. However, I am not good at python script. can you please suggest me what to do with that.

molbiolab@molbiolab:~/Documents/Juli/Practice/cufflinks-2.2.1.Linux_x86_64$ ./cuffmerge
  File "./cuffmerge", line 95
    except getopt.error, msg:
                       ^
SyntaxError: invalid syntax
rna-seq
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updated by Nitin Narwade Nitin Narwade • written by julianasrinjuli • julianasrinjuli

Please avoid the term "dear" - it means different things in different cultures and can be perceived as inappropriate in certain cultures. Also, please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

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written by Ram Ram

thank you for your suggestions. can you please help me regarding the question I have asked??

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written by julianasrinjuli • julianasrinjuli

You need to provide files as input for cuffmerge. If you want to look at the help then generally ./cuffmerge -h (or --help)` is the normal convention for that.

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written by GenoMax GenoMax

couple of things to check make sure you are using python 2.7

python --version
alias python=python2.7

Also, make sure you are not running out of some virtual env with different python version than the system

deactivate

I was able to get rid of the error with the above Hope this helps

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written by aneeshpanoli • aneeshpanoli

1 answer

cuffmerge is written in python. if you run it with ./cuffmerge system will treat cuffmerge as a shell script.

You can run it by python /path/to/cufflink/src/folder/cuffmerge or you can add it in $PATH variable and call it directly like cuffmerge

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written by Nitin Narwade Nitin Narwade

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