outSAMattributes NH HI AS nM CR CY UR UY

注意–outSAMattributes ALL指输出所有tag，如：NH:i:1 HI:i:1 AS:i:202 nM:i:3 NM:i:2 MD:Z:57T14C32 jM:B:c,-1 jI:B:i,-1 MC:Z:45S105M
默认情况下（指不加该参数）只有： NH:i:1 HI:i:1 AS:i:292 nM:i:3 这几个(好像是，待验证)，也可以指定只输出哪几个。因为有些下游分析软件会要求bam中药有NM才能统计。

作者：巴拉巴拉11
链接：https://www.jianshu.com/p/294eadc1fc5a
SAM属性可以由用户使用–outSAMattributes A1 A2 A3…，接受两个字符SAM属性列表的选项。这些属性可以按任何顺序列出，并且按照该顺序记录在SAM文件中。默认情况下，STAR将输出NH HI AS nM等属性。

–outSAMattributes NH HI AS nM CR CY UR UY

CR CY UR UY sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.
https://www.jianshu.com/p/f39c424af326
https://zh.wikibooks.org/wiki/生物信息学/STAR

1Presets: #预先调整
2None : No SAM attributes
3Standard : NH HI AS nM
4All : NH HI AS nM NM MD jM jI MC ch
5Alignment: #比对

6NH : number of loci the reads maps to: = 1 for unique mappers, > 1 for multimappers. Standard SAM tag.
7HI : multiple alignment index, starts with –outSAMattrIHstart (= 1 by default). Standard SAM tag.
8AS : local alignment score, +1/ − 1 for matches/mismateches, score* penalties for indels and gaps. For PE reads, total score for two mates. Standard SAM tag.
9NM : edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.
10nM : number of mismatches per (paired) alignment, not to be confused with NM, which is the number of mismatches+indels in each mate.

11jM:B:c,M1,M2,… : intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical;
121: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions
13database is used, and a junction is annotated, 20 is added to its motif value.
14MD : string encoding mismatched and deleted reference bases (see standard SAM specifications).
15Standard SAM tag.
16jI:B:I,Start1,End1,Start2,End2,… : Start and End of introns for all junctions (1-based).
17jM jI : attributes require samtools 0.1.18 or later, and were reported to be incompatible with
18some downstream tools such as Cufflinks.
19Variation: #变化
20vA : variant allele.
21vG : genomic coordinate of the variant overlapped by the read.
22vW : W ASP filtering tag, see detailed description in Section 11. Requires --waspOutputMode
23SAMtag.

24STARsolo:
25CR CY UR UY : sequences and quality scores of cell barcodes and UMIs for the solo* demulti-
26plexing, not error corrected.
27GX GN : gene ID and name.
28CB UB : error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires
29–outSAMtype BAM SortedByCoordinate.
30sM : assessment of CB and UMI.
31sS : sequence of the entire barcode (CB,UMI,adapter…).
32sQ : quality of the entire barcode.
33Unmapped reads:
34uT : for unmapped reads, reason for not mapping:
350 : no acceptable seed/windows, ”Unmapped other” in the Log.final.out
361 : best alignment shorter than min allowed mapped length, ”Unmapped: too short” in
37the Log.final.out
382 : best alignment has more mismatches than max allowed number of mismatches, ”Un-
39mapped: too many mismatches” in the Log.final.out
403 : read maps to more loci than the max number of multimappng loci, ”Multimapping:
41mapped to too many loci” in the Log.final.out
424 : unmapped mate of a mapped paired-end read