Closed lipikakalson closed 9 months ago
Dear user, This script requires the user to pass a file listing a the tsv files obtained in step 4.1 (not 4.2). It can be run with one file or with multiple (especially if they are generated in a similar manner).
Example of the input file:
Donor1.calling.step1.tsv
Donor2.calling.step1.tsv
Donor3.calling.step1.tsv
We apologise for not specifying this in the repo, as this is a very advanced functionality for a very limited number of people. In any case, we have now provided this info here.
Importantly, and in general terms, all scripts provided in SComatic have the --help
parameter to find the specific documentation of each functionality. So, if you have doubts, you can always run python script_of_interest.py --help
to get the documentation of each script.
Thanks, Fran
Hi Fran, Thank you so much for a detailed explanation. It is working now. I am getting the output.
But it is not estimating the frequency of trinucleotides in my case.
Any idea why is it so?
Thanks, Lipika
Could you print the first lines of the tsv file (step4.1) you use?
Yes, here you go.
What do you get if you run this?
grep -v '^#\|LC_' your.tsv | awk -F'\t' -v OFS='\t' '{if ($19 >= 2 && $20 >= 2) {print $0}}'
Ok! Let's check the next:
And what about this?
grep -v '^#\|LC_' your.tsv | awk -F'\t' -v OFS='\t' '{if ($19 >= 2 && $20 >= 2) {print $4,$8,$9}}'; done | sort -T $PWD | uniq -c | sed 's/^[ \t]*//' | tr ' ' '\t'
Giving syntax error.
During the computation, there should be created a *temp file. Could you paste it here?
Its empty.
Ok, let me try a couple of tests and I will come back to you soon.
The script is working in my example data. Could you try to run it using the example data as well? I put the command at the end of the example documentation
Yes, I tried with Example data, its working perfectly with it. But why not with my data, because all other steps are working fine?
Could you run this and send me the first few hundred lines of the output to me? Maybe by mail?
grep -v '^#\|LC_' your.tsv | awk -F'\t' -v OFS='\t' '{if ($19 >= 2 && $20 >= 2) {print $0}}' > example.tsv
Done
The problem has been solved. This script was required to provide the full path for the output file. Now it has been updated to allow a short path output file.
Hi, I was trying to use the TrinucleotideContextBackground.py. This is ss of my final output file after step 4.2.
This is error while I am using it. This just goes on for a long time.
Am I doing it wrong or there is some other issue?
Thanks, Lipika