xinglab / rmats-stat Goto Github PK

Dear professors：
I met some questions when I run the rmats.py. The version of the rMATS is 'rMATS.4.0.2'. when I run the rmats.py, it would have some errors about "Traceback (most recent call last):
File "/panfs/sugon/home/yanxm/softwares/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/paste.py", line 52, in main()
File "/panfs/sugon/home/yanxm/softwares/rMATS.4.0.2/rMATS-turbo-Linux-UCS4/rMATS_P/paste.py", line 45, in main ofp1.write(line[0]+'\n')
TypeError: 'map' object is not subscriptable". I have tried many times, however ,still unsolved. I hope you can hep me out. I really don't know the reason. I am looking forward to your reply.

Can you briefly mention that how you generate count matrix. Does this refer to outputs generated by rMATS run (which anyway generates differential analysis and statistics). Do you have any utility tool that can generate count matrix without running the whole rMATS.

If the above mentioned option is available, the tool can be scalable with thousand samples. Also, user may not need to know the label (or two group of samples) upfront.

New version of rMATS reports SkipFormLen as read length minus one. In the inc.txt provided with rMATS-STAT, SkipFormLen is different for different events. Here also, could we use read length instead. Could you please clarify my doubt. Your response is highly appreciated.

Hi,

Can you let me know, how is this different from your rMATS package?
Does this need less resources, it is fast etc.

Regards,
Onkar

I notice a problem on the README

$ python FDR.py input > output

I ran the script today and get the error

Traceback (most recent call last):
  File "FDR.py", line 55, in <module>
    ofile=open(sys.argv[2],'w');ofile.write(title[:-1]+'\tFDR\n');
IndexError: list index out of range

the command should be:

$ python FDR.py input output

Then the code works.

Hi,
I noticed that rMATS v4 do not include paired analysis.
Then I used rMATS-STAT scripts to compute the paired analysis and the corresponding FDR based on the *.raw.input.* files

Would it be possible to get a script that take in input the file with FDR and output the equivalent of *.MATS.* files (with gene annotations, events annotations and inclusion levels) ?