input_reads vs full_len_reads in differential_expression()

[mehc555]

Ask away!

Hi,

In main.nf, input_reads is fed to differential_expression() and in differential_expression.nf the workflow differential_expression {} has full_len_reads defined. I've seen workflows that use pychopper reads and then align and quantify gene expr. Here are all input reads used then, or am I wrongly interpreting this?

Thank you

[sarahjeeeze]

Hi, you are correct- thanks for pointing this out we will look in to seeing if it makes sense to update it to use the reads output by pychopper for DE_analysis. This only makes a difference for the direct_rna mode.