===免疫组学TCR分析===

====脚本====

<code>
#python /WORK/Cancer/baiyingnan/01.Neoantigens/V2/HIM_v1.1.py \
python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/Advanced_Analytics/01.Neoantigens/V2/HIM_v1.1.py \
	--infile samplelist.config \
	--analydir `pwd` \
	-g hg19 \
	--analy_array 5.1,5.2 \
	--newjob tcr.job

</code>
其中samplelist.config示例：
<code>
#SampleID	Normal_Bam	State
B_CART	/PAN1/CANCER/Proj/mRNA.X101SC21110642-Z01.immune.X101SC21110642-Z01-F001.20211122/X101SC21110642-Z02-J001-B1-16/bam/B_CART.bam	RNA \\
B_CD137	/PAN1/CANCER/Proj/mRNA.X101SC21110642-Z01.immune.X101SC21110642-Z01-F001.20211122/X101SC21110642-Z02-J001-B1-16/bam/B_CD137.bam	RNA \\
B_CD28	/PAN1/CANCER/Proj/mRNA.X101SC21110642-Z01.immune.X101SC21110642-Z01-F001.20211122/X101SC21110642-Z02-J001-B1-16/bam/B_CD28.bam	RNA \\
</code>
====脚本使用说明====
<code>
python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/Advanced_Analytics/01.Neoantigens/V2/HIM_v1.1.py --help
usage: HIM_v1.1.py [-h] -i INFILE -d ANALYDIR [-a ANALY_ARRAY] [-t HLATYPE]
                   [-j NEWJOB] [-g {hg19,hg38,B37,B38}] [-s SORT] [-f FPKM]
                   [-ft FPKM_THRESHOLD] [-l LENGTH] [-p PURITY]

The analysis module contain hla typing, immune and microenviroment.

optional arguments:
  -h, --help            show this help message and exit
  -i INFILE, --infile INFILE
                        samplelist
  -d ANALYDIR, --analydir ANALYDIR
                        the dir required by analysis results
  -a ANALY_ARRAY, --analy_array ANALY_ARRAY
                        which steps of ananlysis will do. Default (1.1)
                             1    HLA_typing
                              1.1 HLA-HD
                              1.2 polysolver
                              1.3 HLA-PRG-LA
                              1.4 Athlates
                             2    Neoantigens
                             3    Somatic_mutation
                              3.1 SNVINDEL
                              3.2 LOH
                             4    cDNA
                             5    Immune
                              5.1 Trust
                              5.2 Mixcr
                             6    Microenvironment
                              6.1 xCell
                              6.2 IPS
                              6.3 CIBERSORT
                             7    Present
  -t HLATYPE, --hlatype HLATYPE
                        type of HLA: 1 or 2 or 1,2
  -j NEWJOB, --newjob NEWJOB
                        the new job file
  -g {hg19,hg38,B37,B38}, --genome {hg19,hg38,B37,B38}
                        Genome for analysis, default B37
  -s SORT, --sort SORT  sorted by Aff or Rank
  -f FPKM, --fpkm FPKM  fpkm file
  -ft FPKM_THRESHOLD, --fpkm_threshold FPKM_THRESHOLD
                        the threshold of fpkm for annotation of neoantigens
  -l LENGTH, --length LENGTH
                        the half length of peptide around mutational site
  -p PURITY, --purity PURITY
                        purity and ploidy file file including sampleid,2,tumorurity,tumorploidy

</code>

====readme.txt====
<code>
TRUST 软件（Li B， 2017）由刘小乐团队研发，可以从肿瘤 RNA-seq 数据中直接计算免疫组库信息，高通量地精准鉴定肿瘤组织中 TCR 的多样性。 TRUST 采用双端 reads 比对的方式，在算法上优化了 CDR3 序列重组和 unmapped reads 的使用，提高了低丰度 TCR 克隆的检出， 每个样本能够检测出几百到上千的克隆亚型。


(1) Filename：输入的 bam 文件名称
(2) est_clonal_exp： TCR 受体表达量
(3) Vgene： V 基因
(4) Jgene： J 基因
(5) Cgene： C 基因
(6) Reportgene： V/D/J/C 基因位置信息
(7) cdr3aa： CDR3 氨基酸序列
(8) cdr3dna： CDR3 碱基序列
(9) minus_log_Eval：软件预测评分
(10) totaldna： TCR β链碱基序列
(11)contig_reads_count：覆盖的 reads 数量

</code>