Question: What does the "productive" column mean in the contig_annotations.csv file generated by cellranger vdj?
Answer: The "productive" column in all_contig_annotations.csv (or filtered_contig_annotations.csv) identifies contigs that are predicted to generate functional proteins. For a contig to be marked as productive, it must be V-J spanning with a start codon in the leader region. The contig must also have a detectable CDR3 region in frame with the start codon, and be free of stop codons in the V-J spanning region.