Hi!
I have several read groups in my bam files.
By default, it gives me LENGTH_ESTIMATE by each read group.
When I use -m flag, which is supposed to give me the weighted average across read groups weighted by the total number of reads in a group, the LENGTH_ESTIMATE is 5 digits long before the decimal and is no where close to the weighted average I computed manually.
When I use the -u flag, the LENGTH_ESTIMATE value is identical to the weighted average I computed manually. But technically, this flag is supposed to ignore the read groups altogether and is supposed to treat all reads as if from the same read group.
I'm unsure of how to interpret these results.
Also, what is the recommended k threshold for a read length of 150bp?
Hi!
I have several read groups in my bam files.
By default, it gives me LENGTH_ESTIMATE by each read group.
When I use -m flag, which is supposed to give me the weighted average across read groups weighted by the total number of reads in a group, the LENGTH_ESTIMATE is 5 digits long before the decimal and is no where close to the weighted average I computed manually.
When I use the -u flag, the LENGTH_ESTIMATE value is identical to the weighted average I computed manually. But technically, this flag is supposed to ignore the read groups altogether and is supposed to treat all reads as if from the same read group.
I'm unsure of how to interpret these results.
Also, what is the recommended k threshold for a read length of 150bp?