"invalid integer: everything" when trying to run BamToCov

[leone93]

Hi guys I'm trying to use your tool but every option I try to put return this error. invalid integer: "everything"
I'm using the latest versione 2.7 isntalled with Conda.

First I tried with: bamtocov -w -o -T 24 sorted.bam > coverage.wig
and the error was invalid integer: -o
then I removed -o and I have the error invalid integer: -T
then I tried to write --threads instead of -T and invalid integer: --threads
then I left only the -w and the error was invalid integer: sorted.bam

So after some bestemmie I left only the basic command bamtocov sorted.bam > coverage.bed and it works.
Is it a common issue for you?

[telatin]

Dear @leone93
thanks for sharing your experience.

Regarding your first attempt, the -w and -o flags are not a switch, but arguments requiring something. See the docs:

-w, --wig <SPAN>  
-o, --report <TXT>   

So try:

bamtocov -w 250 -o report.txt -T 24 sorted.bam > coverage.wig

[leone93]

Hi @telatin in this ways work, thanks!
Do you know which is the best span value to select? Is 250 based on your experience?

[telatin]

The window selections is based on the actual protocol, the goal and resolution needed. For some applications you might want a very high resolution, at the expense of a large file, in other circumstances you can opt for a large window to have a blurred representation of the coverage.

(The default output of BamToCov is “bedGraph”, that gives the highest resolution needed with the lowest redundancy, but sometimes a Wiggle file can be easier to parse…)