###tcrBiter Usage and Output### ###Author: Lara McGrath ###Date: 8/29/2017 tcrBiter is a python script that can be run from anywhere but must be in the same folder as the included bed files (bed/TRB-hg38.bed) and myFields.alignmentExport.txt Additional Requirements: Python, mixcr, BLAST and bedtools must be installed and in the path correctly. Additional Requirements: must have BLAST database of hg38 or create one using makeblastdb. Usage: python /path/to/runTCRbiter.py /path/to/some_R1.fastq.gz /path/to/some_R2.fastq.gz /path/to/BLAST/db/for/hg38 tcrBiter creates two directories: tcrError/ tcrOutput/ The following files are made in tcrError/ bedtoolsintersect.read1.error.txt blastcleanread1.error.txt blastread1.error.txt intersectBlastMerge.error.txt MixcrExport.error.txt bedtoolsintersect.read1.stdout.txt blastcleanread1.stdout.txt blastread1.stdout.txt intersectBlastMerge.stdout.txt MixcrExport.stdout.txt bedtoolsintersect.read2.error.txt blastcleanread2.error.txt blastread2.error.txt MixcrAlign.error.txt MixcrFiltering.error.txt bedtoolsintersect.read2.stdout.txt blastcleanread2.stdout.txt blastread2.stdout.txt MixcrAlign.stdout.txt MixcrFiltering.stdout.txt The following files are made in tcrOutput/ filename.alignmentReport.log filename.filteredStats.pdf filename.read1.filtered.fasta filename.results.csv filename.description.txt filename.intersectMerged.txt filename.read1.intersectBed.txt filename.results.curated.csv filename.filteredread1.readkey.txt filename.intersectStats.txt filename.read2.bed filename.results.txt filename.filteredread1.txt filename.intersectVDJ.txt filename.read2.blastClean.txt filename.statsFiltered.csv filename.filteredread2.readkey.txt filename.read1.bed filename.read2.blast.txt filename.vdjca filename.filteredread2.txt filename.read1.blastClean.txt filename.read2.filtered.fasta tcrCommands.txt filename.filteredResults.csv filename.read1.blast.txt filename.read2.intersectBed.txt Important results files are: filename.intersectStats.txt #Defines number of read pairs in: (1) total, (2) with VDJ rearrangment, (3) with only V genes, (4) with only J genes, (5) with one V gene, (6) with one J gene, (7) rearrangement found in single read, (8) rearrangement split across pair filename.intersectVDJ.txt #Breaks down features of each rearranged read Other results files include: filename.alignmentReport.log #MiXCR alignment output report filename.description.txt #Information on how many reads were aligned, filtered, and had defined CDR3 regions filename.filteredStats.pdf #Displays histograms of features of aligned reads