Stop codon found

[linuxbioinfoguy]

Hi, I am a beginner in using this package, just take a try, so in the final report tsv file, there are multiple result from the same asembleid, but with slightly different in the nt and the aa, such as following:
31 6.609808e-02 TGTCAACAGAGTTACAGTACCCCGTACACTTTT CQQSYSTPYTF IGKV1-3901 . IGKJ201 IGKC assemble0 0
12 2.618337e-02 TGTCAATAGAGTTACAGTACCCCGTACACTTTT CQ_SYSTPYTF IGKV1-3901 . IGKJ201 IGKC assemble0 0
9 2.072495e-02 TGTCAACAGAGTTACAGTACCCCGTATACTTTT CQQSYSTPYTF IGKV1-3901 . IGKJ201 IGKC assemble0 0

as see, there is a stop codon TAG in the second sequence and show as CQ_SYSTPYTF. Could this kind of result be considered as false? since quite unlikely a valid sequence contains a stop codon at this part, thanks!

[mourisl]

Since there are multiple reads supporting this stop codon, I believe this is real. This could be introduced by somatic hypermutations resulting in a non-productive receptor. You may filter those non-productive or keep them depending on your analysis.

Each assemble_id encodes highly similar CDR3s (most likely from somatic hypermutation), and this is what is observed here.

[linuxbioinfoguy]

Thanks!