missing mtDNA-CN results in the output file "count.tab"

[FL512]

Hi,

Sorry for keep bothering you but I have encountered another issues, which "count.tab" file does not include all the samples' results analyzed.
It is weird to me because each output folders/files are generated and saved.
So my question is how and where can I get the result of "mtDNA-CN" from individual file that are summarized in the "count.tab" file?
I want to find out the each mtDNA-CN result by looking at the files that are missing in the "count.tab" file to save my analysis.

Thank you!

[dpuiu]

Hi FL512/

I'm so sorry about the delay in getting to this.

First, could you check whether your sample count files have been generated and contain the expected read counts?

Then, you could run getCN.pl (the script that generates the mtDNA copy number) manually. See the example below.

##############################################################

$ ls -l out/*/*count
out/sample_A/sample_A.count
out/sample_B/sample_B.count
...

$ cat out/*/*count | perl -ane 'print if($.==1 or !/^Run/);' | getCN.pl > out/count.tab
$ cat out/count.tab
Run all_reads mapped_reads MT_reads mtDNA-CN
sample_A 222846 222846 221485 363733
sample_B 222817 222817 221539 363869
...