some question about pychopper

[hugs314]

Hi, I want to ask for help with some problems I don't understand 1. Can the current version of PyChopper add the --trim_barcodes parameter during barcoding? 2. when running minimap2 with add --uf ??? 3. Do pychopper processed reads are stranded? When using stringtie should we specify --rf or --fr or none??? 4. I'm not quite sure what this command does ? seqkit bam -j 20 -x -T 'AlnContext: { Ref: "hg38.fa", LeftShift: -24, RightShift: 24, RegexEnd: "[Aa]{8,}", Stranded: True, Invert: True, Tsv: "alignments/internal_priming_fail.tsv"} ' - can you answer it? Thank you very much