Defiant can't find dmr
khl0798 opened this issue · 10 comments
I was running defiant and can't find any dmr areas. I don't know why I can't find the dmr area, I really want to know why.
Input file is as follows：
columns are chromosome，cpgstart，cpgend，methylation percent，coverage
Run the command as follows：
/data/home/hlkong/defiant-master/defiant -p 0.5 -v -FDR -l aaaa -L p.Recurrence,n.No_Recurrence -i control1,control2,control3 case1,case2,case3
Server configuration：
Defiant version:
Results：
### log file ：
defiant_run_info_aaaa.txt.txt
Hi @khl0798 this isn't one of the recognized 11 formats. It could easily be converted, however. Do you need help converting to one of these formats? I can write a script for you if you like.
Hi @khl0798 this isn't one of the recognized 11 formats. It could easily be converted, however. Do you need help converting to one of these formats? I can write a script for you if you like.
Many thanks. I changed the input file format as follows:
the columns are chromosome, cpg start, cpg end, methylation percent, coverage.
but still can't find dmr area.
results and log info as follows:
p.Recurrence_vs_n.No_Recurrence_Recurrence_vs_No_Recurrence_c10_CpN5_d1_p0.05_P10.txt
Hi @khl0798 I'll write a script for you to convert the data by the end of the day Central Standard Time. I'll convert to input format 4.
Hi @khl0798
make_input_format4.txt
I've attached this perl script (it has to be ".txt" not ".pl" because GitHub is stupid) which will translate files from the format you gave.
run it like this: "perl make_input_format4.txt file1 file2 file3 ...." and each new file will have a ".format4" attached to the end of the file name.
Let me know how it goes,
-Dave
Hi @khl0798
make_input_format4.txt
I've attached this perl script (it has to be ".txt" not ".pl" because GitHub is stupid) which will translate files from the format you gave.run it like this: "perl make_input_format4.txt file1 file2 file3 ...." and each new file will have a ".format4" attached to the end of the file name.
Let me know how it goes,
-Dave
Thanks. I have changed the input file format:
the columns are chromosome, cpg start, methylated C count, coverage.
Howerver, there is no dmr in the output file:
the log file:
defiant_run_info_Recurrence_vs_No_Recurrence.txt
p.Recurrence_vs_n.No_Recurrence_Recurrence_vs_No_Recurrence_c10_CpN5_d1_p0.05.txt
Hi @khl0798
try lowering the thresholds for DMRs, for example "-CpN 4" or "-P 5" or lower the coverage threshold with "-c 5" or something like that. There are many options to make Defiant more or less sensitive. You can see the list of options with '-help'.
-Dave
Hi @khl0798
try lowering the thresholds for DMRs, for example "-CpN 4" or "-P 5" or lower the coverage threshold with "-c 5" or something like that. There are many options to make Defiant more or less sensitive. You can see the list of options with '-help'.
-Dave
hi . @hhg7 . I changed some options like "-P 3 -c 3 -CpN 3", however still can't find the dmr.
The following are the result files.
I can't understand when I set "-c 3 -CpN3 ", 206439/5616948 = 3.7% of nucleotides met minimum coverage and were present with minimum coverage = 3 in every sample.
I used R to compute one sample “1PT_CpG_meth.txt”.
I find that more than 40% of cpg region has coverage more than 10.
Can you leave a mailbox? It is convenient for me to send the data to you. I want you to help me run it. All the data is probably more than 500M. I am very grateful.
Hi @khl0798 my email is dec986@gmail.com I'm happy to help out if I can
Hi @khl0798 my email is dec986@gmail.com I'm happy to help out if I can
HI @hhg7 . I sent the data to your “dec986@gmail.com” mailbox. Thank you very much for your help.
Hi @khl0798 my email is dec986@gmail.com I'm happy to help out if I can
hi @hhg7. Do you receive the data I sent you? If you are convenient, can you tell me if the result is running out?