No annotated mol in final output

[mimidu]

Hi,

Thank you for your hard work and clear instruction. I ran through the pipeline and got the final count table. But there is no annotated molecules:

#samples LIB4854636_SAM24358596
#unannotatedmolc 121188
#annotatedmolc 0

It should not be since I have spike-ins.

I checked the bam files and it looks like I have hits actually, but it did not show up in the final table:

I suspect the problem is in the "Count molecules and merge into single file" step. I attached my GenePred file(modified from mirBase ff3 file).

mmu_2.txt

One thing i noticed is that my reads(around 20nt) are much shorter than yours. Any suggestions?

thanks and best,

Lily