Hello Kathy,
To confirm, this was run on the public Main Galaxy instance at
https://main.g2.bx.psu.edu/ (usegalaxy.org ?).
It could be that your intervals are overlapping with a gap region (a
known gap, padded with "N's" - there are are several classes). This
could be quickly checked by view
Hi,
I'm having trouble with the Generate Pileup tool and hope that you could
help me troubleshoot this. I ran the tool successfully with the
following options:
* Use built-in index
* Print the mapping quality as the last column
* Print all lines
* Cap mapping quality =
Can we use the SAM tools pileup tool in Galaxy to get an accurate count of
the coverage across the genome? I ask because I have run the pileup tool
in Galaxy with bam files generated from tophat and noticed that the
coverage reported in the pileup data was consistently lower then what I
see in I
Can we use the SAM tools pileup tool in Galaxy to get an accurate count of the coverage across the genome? I ask because I have run the pileup tool in Galaxy with bam files generated from tophat and noticed that the coverage reported in the pileup data was consistently lower then what I see in I
4 matches
Mail list logo
