Question: How to run a Alternative Splice Junction analysis ?
0
gravatar for CriticalPeriod
6 days ago by
CriticalPeriod0 wrote:

Hello everyone, I am totally new to bioinformatics and programming, but i'm sure it's the future of science and I am determined to learn .

So I will try to explain my problem, and maybe someone can help me. I have RNA-seq data, already processed and analyzed. So I have bam/bai files in a directory, and excel files with readable results of diff. expressed genes between my two conditions.

I found a program on Git Hub, name spladder https://github.com/ratschlab/spladder which should do more or less what I want, i.e find if there is differents splicing variants between my two conditions. Maybe there is better tools, if someone knows one...

The problem is that I can't even run the program, it must be something stupid but i'm totally new, and this is a nightmare for me. I'm running on Mac OS, latest version (mojave). I've installed anaconda3 on my mac, and I have a directory name anaconda3 in my harddrive, along with user, system etc.

I used git clone on my terminal to clone the repository of spladder on github. It appears in a depository name projects on my "user" page , with downloads, documents etc.

When i try to run python spladder.py in terminal, I have : :~ user$ python3 spladder.py python3: can't open file 'spladder.py': [Errno 2] No such file or directory

my PATH is user$ echo $PATH /anaconda3/bin:/miniconda3/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

I tried to copy/past the "projects" directory in anaconda3 file, but it changed nothing. I think there is a very simple thing I miss here...

I hope someone can help, with a lot of gratitude, Thanks

ADD COMMENTlink written 6 days ago by CriticalPeriod0

Does python /path/to/where/you/git/cloned/spladder/python/spladder.py work?

ADD REPLYlink written 6 days ago by cschu1811.5k
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