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I have a question about the output from AIRRflow, ...
# airrflow
m
I have a question about the output from AIRRflow, I've noticed that in the fwr 1-4 and cdr 1-3 columns of the BCR output it will often just put the start and end of the sequence (separated by ...) but not the full fwr1-4 or cdr1-3 sequence. Is there a parameter setting to change these to properly output the actual subset of the sequence that it is referring to? Especially since in some cases the end sequence is only three nucleotides which is insufficient for matching to the origin sequence. @Gisela Gabernet
g
Regarding the FWR and CDR region nucleotide sequences, they should be in the final repertoire dataframe (e.g. inside the 
define_clones
) folder. Aren’t they there for you? If not, could you share the command you used for running the pipeline?
m
You are referring to the subject_x__clone-pass.tsv, within define_clones and repertoire, correct? The "sequence" field is a complete sequence, but the cdr1, cdr2, etc sequences are shown with the ... between the start and the end nucleotides and do not show a complete sequence.
It is this file in my data analysis directory
This is the command I used to run AIRRFlow @Gisela Gabernet
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nextflow run nf-core/airrflow -r 4.1.0 -profile biowulf --input Ainhoa_BCR_SampleSheet.tsv --mode assembled  --outdir Jun132024run_AinhoaBCR_results_igphyml --cloneby subject_id --lineage_trees --lineage_tree_builder igphyml --lineage_tree_exec /data/homc/igphyml/src/igphyml
g
Hi Margaret, this is a complete sequence but it contains what are called the IMGT gaps, which represent all of the VDJ sequences with the same positions to be able to compare the positions on different BCRs that might be e.g. IGHV1 or IGHV3. If you would like to have the ungapped sequences, you can just remove the “.” in these columns and these will be the full FWR and CDR sequences
m
Oh! That is very helpful information, thank you very much!
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