Running ImReP

ImReP help message

In order to see ImReP help message, invoke

$ python imrep.py -h

from the command line.

Necessary parameters

• reads_fastq - file with RNA-Seq or TCR-(BCR-)-Seq reads in .fastq format. If the reads are paired, then you must ensure that they are stored in one file.

• output_clones - output file.

Optional parameters

• -o OVERLAPLEN, --overlapLen OVERLAPLEN - the minimal length to consider between reads overlapping with a V gene and reads overlapping with a J gene. Default value is 10 amino acids.

• --noOverlapStep - a binary flag used in case if the user does not want to run the second stage of the ImReP assembly.

• -t CASTTHRESHOLD - a custom parameter which controls the stringency of CDR3 clustering. Current version of ImReP uses CAST clustering algorithm for building clonotypes. The default value is 0.2

• -c CHAINS, --chains CHAINS - comma separated value of chains to search for. The default value is IGH,IGK,IGL,TRA,TRB,TRD,TRG.