where should I found the meaning of results' header

[gnili...@gmail.com]

Dear author,

    I have been use CTK to my analysis, but parts of header in the results are hard to understand.

   Such as, results of `CIMS.pl`, what's the meaning of 'count(>m,k). Apparently, it's not the reads count of the mutation site.

   So, where should I found the meaning of results' header ?

   Thank you for your jobs.

[Huijuan Feng]

Hi,

Thanks for choosing CTK.

The count(>m, k) is the number of clustered mutation sites with k tags and have >=m mutation frequency. We calculated to cumulative number to estimate the FDR. 

For example, if the site has k=15 and m=2, then count(>m, k) is the total sites number with m>=2 and k=15. You can get the same results using this command:

awk '{if($7>15&&$8>=2)print}' cims.output | wc -l

For more information, you can refer to the examples here:

https://zhanglab.c2b2.columbia.edu/index.php/ICLIP_data_analysis_using_CTK.

Please let me know if you have more questions.

Thanks!