Hello all,
I would like to know if someone knows what is causing this message when I am using samview in order to retrieve all the reads that are falling in that region?
[main_samview] region "chr2:63209526-63209337" could not be parsed. Continue anyway.
I am using this command :
samtools view $aligmentFile $region | cut -f1
Where $aligmentFile
is my bam file and the $region
is one of the several regions that I want to retrieve the reads.
For some regions, it works fine, but I have this message for several of them.
Thanks in advance for your responses,
Can you post the complete command you are using?
Oh sure!! Sorry, I forgot. It is done now.
So, like, samtools view.
Hello Marvi,
make sure you have a
chr2
. I guess your chromosome names are not prefixed withchr
. So the name is just2
.fin swimmer