CPM(counts per M reads) for cuffdiff --max-bundle-frags will be better when different seq depth?

[wangyugui]

Hi.

CPM(counts per M reads) for --max-bundle-frags will be better when different seq depth?

When the total reads is 25M and --max-bundle-frags is 500K, then the CPM value will be 20K.

[wangyugui]

maybe 0.002 will be better than 20K CPM.

if we use 0.002 , then we will not need a new param interface.

[wangyugui]

we can set different --max-bundle-frags for every bam when cufflinks. but we have to set one value for cuffdiff with multiple bam file.