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Running ImReP
In order to see ImReP help message, invoke
$ python imrep.py -h
from the command line.
##Necessary parameters
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reads_file - file with RNA-Seq or TCR-(BCR-)-Seq reads in .fastq or .fasta format. If the reads are paired, then you must ensure that they are stored in one file.
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output_clones - output file.
##Optional parameters
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--fastq, a binary flag used to indicate that the input file with unmapped reads is in fastq format
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-s SPECIES, --species SPECIES - species (human or mouse, default human).
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-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.
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--noOverlapStep - a binary flag used in case if the user does not want to run the second stage of the ImReP assembly.
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-t CASTTHRESHOLD - the -t option has been added to control the stringency of CDR3 clustering. The value can be from 0.0 to 1.0. Note that thresholds near 1.0 are more liberal and result in more CDR3 to be reported. The default value is 0.2
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-c CHAINS, --chains CHAINS - comma separated value of chains to search for. The default value is IGH,IGK,IGL,TRA,TRB,TRD,TRG.
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-extendedOutput - if this option is set, ImReP will produce two additional files: full_cdr3.txt and partial_cdr3.txt containing detailed information for each read (V(D)J recombination and CDR3 it comes from)