Defiant can't find dmr

[khl0798]

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

[hhg7]

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.

[khl0798]

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

defiant_run_info_Recurrence_vs_No_Recurrence.txt

[hhg7]

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.

[hhg7]

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

[khl0798]

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

[hhg7]

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

[khl0798]

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.

[hhg7]

Hi @khl0798 my email is [email protected] I'm happy to help out if I can

[khl0798]

Hi @khl0798 my email is [email protected] I'm happy to help out if I can

HI @hhg7 . I sent the data to your “[email protected]” mailbox. Thank you very much for your help.

[khl0798]

Hi @khl0798 my email is [email protected] 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?