i am trying to analyze paired end NGS CRISPR Screen Data using the Mageck Flute Pipeline.
After running fastqc and fastq groomer, I used cutadapt to trim adapter sequences.
When using Mageck count, I get this error: Cannot automatically determine the --trim-5 length. Only 0.0 % of the reads can be identified
Maybe there is something wrong with the adapter trimming already? I also tried trim galore but got the same error when performing Mageck count.
Thanks, I appreciate your help!