Antigen receptor repertoires profiling from RNA-Seq

<b>TCGA_SKCM_clinical_data_metadata_and_clonesets.xlsx</b> - 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).<br><br><b>CoverageStat.tsv</b> - 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.<b><br></b><b>Sorted_mice_TCR_clonesets.zip</b> - TCR clonesets for sorted mouse cell populations from section "Functional characterization of TRA and TRB repertoires based on RNA-Seq of sorted T-cells"<b><br></b><b>Data for comparison of MiXCR with TRUST and V'DJer on real data</b><br><b><br></b><b>SamplesForComparison.tsv</b> - 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 <b>Figure 2e</b>.<br><b>analysis_results.zip</b> file contain all analysis results for all samples listed in SamplesForComparison.tsv. See <b>README.txt</b> file for exact commands used to generate this data. Archive has the following folder structure:<br><i>rnaseq/mixcr</i> - 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 + IGK<br>ALL = all chainsTab-separated table. Unprocessed MiXCR output.<br><i>rnaseq/trust</i> - 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.<br><i>rnaseq/vdjer</i> - analysis results for V'DJer. fasta files. Unprocessed V'DJer output.<br><br><i>repseq</i> - clonotypes from control TCR-Seq datasets assembled using MiXCR software with default settings.<br><br><i>notebooks</i> - contains IPython notebook for final data anaylsis and figure generation<br><br><i>scripts</i> - contains python and shell scripts to convert software-specific formatted data into msgpack format that is used by IPython notebook mentioned above<br><br><br>See also https://github.com/milaboratory/mixcr-rna-seq-paper repository for the code for <i>in-silico</i> experiments.