ImReP output

ImReP output is tab separated file consisting of the following fields:

• CDR3 amino acid sequence (we refer to it as clonotype)

• Read count supporting the clonotype

• V gene

• D gene

• J gene

Also, for an extended output of ImReP, please run the following command:

$ python imrep.py unmappedReads.fastq output.txt --extendedOutput

Two additional files will be generated:

• full_cdr3.txt - full CDR3 output

• partial_cdr3.txt - partial CDR3 output, i.e. reads having intersecting either a V or a J gene

Both files provide information for each read, i.e. for each read the user can trace CDR3 region it comes from. More detailed, both files have the following format:

• Field 1: read name

• Field 2: CDR3 sequence (full CDR3 in full_cdr3.txt and partial CDR3 for partial_cdr3.txt) it takes part in

• Field 3: V chain

• Field 4: D chain

• Field 5: J chain

• Field 6: comma separated list of V gene alleles the read intersects with. Each item in the list has the format "allele_name:overlap_aminoacids:mismatches_aminoacids"

• Field 7: comma separated list of J gene alleles the read intersects with. Each item in the list has the format "allele_name:overlap_aminoacids:mismatches_aminoacids"

• Field 8: binary flag. Equals 1 if the list in Field 6 has only one item. 0 otherwise

• Field 9: binary flag. Equals 1 if the list in Field 7 has only one item. 0 otherwise

• Field 10: binary flag. Equals 1 if V and J alleles are determined uniquely. Equal to (Field 8) & (Field 9)