10Xgenomic cellranger 结果文件“filtered_contig_annotations.csv”

每一行的意义

https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/output/annotation#contig

filtered_contig_annotations_列名.png

Productive Contigs

一条contig被称作是productive 需要满足以下条件：

需要全长：

这条contig需要以Vgene起始，以J基因结束（CDR3的结构（VDJ））

起始要求：

Vgene的起始部分需要为起始密码子。在10X测序中，人类和小鼠参考序列，每个Vgene都是以起始密码子开始；

非终止需要：

一条contig 在V起始和J结束间无终止密码子

读码框内要求：

V起始和J结束的碱基为3的倍数；

必须为CDR3:

Let VJ denote the sum of the lengths of the V and J segments. Let len denote the J stop minus the V start, measured on the contig. Then VJ - len lies between -25 and +25, except for IGH, which must be between -55 and +25. This condition is imposed to preclude anomalous structure changes that are unlikely to correspond to functional proteins.
解释：必须是在一定长度范围的contig才算CDR3

barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id
AAACCTGGTGACGCCT-1,True,AAACCTGGTGACGCCT-1_contig_1,True,506,TRB,TRBV11-3,None,TRBJ2-3,TRBC2,True,True,CASSSGGREDYTDTQYF,TGTGCCAGCAGCTCAGGGGGGCGGGAGGACTACACAGATACGCAGTATTTT,3458,12,clonotype118,clonotype118_consensus_1
AAACCTGTCCTTTCGG-1,True,AAACCTGTCCTTTCGG-1_contig_1,True,530,TRA,TRAV27,None,TRAJ44,TRAC,True,True,CAGSNTGTASKLTF,TGTGCAGGGTCAAATACCGGCACTGCCAGTAAACTCACCTTT,19476,5,clonotype4,clonotype4_consensus_1
AAACCTGTCCTTTCGG-1,True,AAACCTGTCCTTTCGG-1_contig_2,True,654,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSILPRNEQFF,TGTGCCAGTAGTATACTACCACGAAATGAGCAGTTCTTC,23576,8,clonotype4,clonotype4_consensus_2
AAACCTGTCCTTTCGG-1,True,AAACCTGTCCTTTCGG-1_contig_3,True,480,TRA,TRAV36/DV7,None,TRAJ45,TRAC,True,False,None,None,4284,1,clonotype4,None
AAACCTGTCCTTTCGG-1,True,AAACCTGTCCTTTCGG-1_contig_4,True,321,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,2316,3,clonotype4,None