Antigen receptor repertoires profiling from RNA-Seq

TCGA_SKCM_clinical_data_metadata_and_clonesets.xlsx - Immune repertoires and sample metadata from the TCGA 48+48 nt paired-end RNA-Seq data for 460 patients with human skin cutaneous melanoma (SKCM).CoverageStat.tsv - data for calculation of TCR CDR3 extraction performance characteristics in respect to different TCR content, read-length and dataset type (single- or paired- end). Data for Supplementary Table 2.Sorted_mice_TCR_clonesets.zip - TCR clonesets for sorted mouse cell populations from section "Functional characterization of TRA and TRB repertoires based on RNA-Seq of sorted T-cells"Data for comparison of MiXCR with TRUST and V'DJer on real dataSamplesForComparison.tsv - list of all RNA-Seq samples used for MiXCR / V'DJer / TRUST comparison, including samples obtained by truncation of samples with longer read length. Summary analysis statistics for each sample. Tab-separated table. Data for Figure 2e.analysis_results.zip file contain all analysis results for all samples listed in SamplesForComparison.tsv. See README.txt file for exact commands used to generate this data. Archive has the following folder structure:rnaseq/mixcr - results of RNA-Seq samples using MiXCR. Individual files for each immunological chain: TRA, TRB, TRG, TRD, IGH, IGL, IGK.Combined data:TCR = TRA + TRB + TRG + TRDIG = IGH + IGL + IGKALL = all chainsTab-separated table. Unprocessed MiXCR output.rnaseq/trust - analysis results for TRUST. fasta files (some files are prepended with comment blocks, each line in comment block starts with #). Each file accumulate sequences for all chains (TRA + TRB + TRG + TRD). Unprocessed TRUST output.rnaseq/vdjer - analysis results for V'DJer. fasta files. Unprocessed V'DJer output.repseq - clonotypes from control TCR-Seq datasets assembled using MiXCR software with default settings.notebooks - contains IPython notebook for final data anaylsis and figure generationscripts - contains python and shell scripts to convert software-specific formatted data into msgpack format that is used by IPython notebook mentioned aboveSee also https://github.com/milaboratory/mixcr-rna-seq-paper repository for the code for in-silico experiments.