Closed leone93 closed 2 years ago
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
Hi @telatin in this ways work, thanks! Do you know which is the best span value to select? Is 250 based on your experience?
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…)
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.bamSo after some bestemmie I left only the basic command
bamtocov sorted.bam > coverage.bed
and it works. Is it a common issue for you?