Following on from the data I was looking at last week, I have added an additional flag to the ReadStats.sh script so that poor quality data is identified, and the reason for the problems can be tracked down. The script now tests that the proportion of reads that get through the trimmomatic quality screening is >60% (anything below this suggests a problem with the sequencing instruments).
I came across another issue which meant that any values below 1 caused an error when using the standard [ command. In Ubuntu #!/bin/sh calls dash by default, so now bash is called explicitly and [ is replaced with [[
Following on from the data I was looking at last week, I have added an additional flag to the ReadStats.sh script so that poor quality data is identified, and the reason for the problems can be tracked down. The script now tests that the proportion of reads that get through the trimmomatic quality screening is >60% (anything below this suggests a problem with the sequencing instruments).
I came across another issue which meant that any values below 1 caused an error when using the standard
[command. In Ubuntu #!/bin/sh calls dash by default, so now bash is called explicitly and[is replaced with[[