I am trying to use the Kneaddata to remove the host mRNA (fish) and keep the microorganisms mRNA. However, after running the Kneadata the output is empty. Here is the log file. I used these sequences for host gene expression and everything worked well (with host reference and bowtie, etc.) but in here it looks like it is an alignment issue.
67A_R1_kneaddata.txt (28.9 KB)