10Xgenomic cellranger 結(jié)果文件“filtered_contig_annotations.csv”

每一行的意義

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

filtered_contig_annotations_列名.png

Productive Contigs

一條contig被稱作是productive 需要滿足以下條件：

需要全長(zhǎng)：

這條contig需要以Vgene起始，以J基因結(jié)束（CDR3的結(jié)構(gòu)（VDJ））

起始要求：

Vgene的起始部分需要為起始密碼子。在10X測(cè)序中，人類和小鼠參考序列，每個(gè)Vgene都是以起始密碼子開(kāi)始；

非終止需要：

一條contig 在V起始和J結(jié)束間無(wú)終止密碼子

讀碼框內(nèi)要求：

V起始和J結(jié)束的堿基為3的倍數(shù)；

必須為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.
解釋：必須是在一定長(zhǎng)度范圍的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