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,
•
written
by
MarVi •
1 answer
chr2:63209526-63209337
The begin of your interval is larger than the end, so that interval is invalid.
Haha yeah it's obvious as soon as you see it, but can be very puzzling :)
FYI:
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Happy to help!
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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