Computational protocol: Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

Similar protocols

Protocol publication

[…] Paired-end reads from the 91 single-cell RNAseq samples were mapped simultaneously to the Mus musculus genome (Ensembl version 38.70) and we counted reads for each gene using htseq-count [] to generate a raw counts table of genes across all 91 samples. The raw counts were then processed and filtered according to the edgeR vignette [] and the unadjusted FPKM for each gene was calculated as its cpms (counts per million (CPM) mapped reads) normalized by the summed length of its exons. […]

Pipeline specifications

Software tools HTSeq, edgeR
Application scRNA-seq analysis
Diseases Neoplasms