{"id":421,"date":"2019-08-16T10:20:45","date_gmt":"2019-08-16T02:20:45","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=421"},"modified":"2019-08-20T13:00:22","modified_gmt":"2019-08-20T05:00:22","slug":"cellranger%e4%bd%bf%e7%94%a8%e6%95%99%e7%a8%8b","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=421","title":{"rendered":"Cellranger\u4f7f\u7528\u6559\u7a0b"},"content":{"rendered":"

\u5efa\u5e93\uff0c\u4eba\u548c\u5c0f\u9f20\u7684\u6570\u636e\u5e93\u53ef\u4ee5\u76f4\u63a5\u4e0b\u8f7d\uff0c\u5bf9\u4e8e\u65e0\u6cd5\u76f4\u63a5\u4e0b\u8f7d\u7684\u9700\u8981\u81ea\u884c\u4e0b\u8f7d\u5168\u57fa\u56e0\u7ec4\u5e8f\u5217\u548cgtf\u6587\u4ef6\uff0c\u6839\u636e cellranger mkref\u6784\u5efa\u53c2\u8003\u6570\u636e\u5e93<\/p>\n

wget ftp:\/\/ftp.ensembl.org\/pub\/release-97\/fasta\/danio_rerio\/dna\/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz\r\ngunzip Danio_rerio.GRCz11.dna.primary_assembly.fa.gz\r\nwget ftp:\/\/ftp.ensembl.org\/pub\/release-97\/gtf\/danio_rerio\/Danio_rerio.GRCz11.97.gtf.gz\r\ngunzip Danio_rerio.GRCz11.97.gtf.gz\r\ncellranger mkgtf Danio_rerio.GRCz11.97.gtf Danio_rerio.GRCz11.97.filtered.gtf                  \r\n                 --attribute=gene_biotype:protein_coding \\\r\n                 --attribute=gene_biotype:lincRNA \\\r\n                 --attribute=gene_biotype:antisense \\\r\n                 --attribute=gene_biotype:IG_LV_gene \\\r\n                 --attribute=gene_biotype:IG_V_gene \\\r\n                 --attribute=gene_biotype:IG_V_pseudogene \\\r\n                 --attribute=gene_biotype:IG_D_gene \\\r\n                 --attribute=gene_biotype:IG_J_gene \\\r\n                 --attribute=gene_biotype:IG_J_pseudogene \\\r\n                 --attribute=gene_biotype:IG_C_gene \\\r\n                 --attribute=gene_biotype:IG_C_pseudogene \\\r\n                 --attribute=gene_biotype:TR_V_gene \\\r\n                 --attribute=gene_biotype:TR_V_pseudogene \\\r\n                 --attribute=gene_biotype:TR_D_gene \\\r\n                 --attribute=gene_biotype:TR_J_gene \\\r\n                 --attribute=gene_biotype:TR_J_pseudogene \\\r\n                 --attribute=gene_biotype:TR_C_gene\r\ncellranger mkref --nthreads=80 --genome=ref_zebr_GRCz11 --fasta=Danio_rerio.GRCz11.dna.primary_assembly.fa --genes=Danio_rerio.GRCz11.97.filtered.gtf --ref-version=3.1.0 \u00a0 \u00a0#\u6ce8\u610fgene_id\u548ctranscript_id\u7684\u987a\u5e8f<\/pre>\n
\u8ba1\u7b97\u8868\u8fbe\u91cf\uff0c\u4e0b\u673a\u7684\u539f\u59cb\u6570\u636e\u53ef\u4ee5\u901a\u8fc7bcl2fastq\u62c6\u5206\uff0c\u4e5f\u53ef\u901a\u8fc7cellranger\u81ea\u5e26\u7684mkfastq\u547d\u4ee4\u62c6\u5206\u3002bcl2fastq\u62c6\u5206\u540e\u5f97\u5230\u4e24\u4e2afastq\u6587\u4ef6\uff0cindex\u4fe1\u606f\u5305\u542b\u5728\u7b2c\u4e00\u4e2afastq\u6587\u4ef6\u7b2c\u4e00\u884c\u5c3e\u90e8\uff1bmkfastq\u62c6\u5206\u540e\u5f97\u5230\u4e09\u4e2afastq\u6587\u4ef6\uff0cindex\u4fe1\u606f\u5305\u542b\u5728\u4e00\u4e2a\u5355\u72ec\u7684fastq\u6587\u4ef6\u91cc\u3002\u4e24\u79cd\u62c6\u5206\u7ed3\u679c\u90fd\u53ef\u4f5c\u4e3acount\u547d\u4ee4\u7684\u8f93\u5165\uff0c\u4f46\u6587\u4ef6\u7684\u547d\u540d\u4e00\u5b9a\u8981\u4e25\u683c\u5b89\u88c5\u8f6f\u4ef6\u7684\u8bf4\u660e\uff0c\u5426\u5219\u4f1a\u51fa\u9519\u3002<\/p>\n
cellranger count --id=PBLzebr1 --transcriptome=\/home\/wuchangsong\/sc_cell\/ref_zebr_GRCz11 --fastqs=\/home\/wuchangsong\/sc_cell\/fastq\/ --sample=PBLzebr1<\/pre>\n
\u5f97\u5230\u7684\u8868\u8fbe\u77e9\u9635\u5728filtered_feature_bc_matrix\u6587\u4ef6\u5939\u4e2d\uff0c\u5728analysis\u6587\u4ef6\u5939\u4e2d\u6709PCA\u548ctSNE\u805a\u7c7b\u7ed3\u679c\u6587\u672c\u5f62\u5f0f\u3002cellranger count \u8ba1\u7b97\u7684\u7ed3\u679c\u53ea\u80fd\u4f5c\u4e3a\u9519\u7565\u89c2\u6d4b\u7684\u7ed3\u679c\uff0c\u5982\u679c\u9700\u8981\u8fdb\u4e00\u6b65\u5206\u6790\u805a\u7c7b\u7ec6\u80de\uff0c\u8fd8\u9700\u8981\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\uff0c\u8fd9\u91cc\u4f7f\u7528\u5b98\u65b9\u63a8\u8350 R \u5305\uff08Seurat\uff09\uff0c\u540e\u8fb9\u7684\u5206\u6790\u53c2\u8003Seurat\u7684\u4f7f\u7528\u3002<\/p>\n
\u53c2\u8003\uff1ahttps:\/\/support.10xgenomics.com\/single-cell-gene-expression\/software\/release-notes\/build#GRCh38mm10_3.1.0<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
\u5efa\u5e93\uff0c\u4eba\u548c\u5c0f\u9f20\u7684\u6570\u636e\u5e93\u53ef\u4ee5\u76f4\u63a5\u4e0b\u8f7d\uff0c\u5bf9\u4e8e\u65e0\u6cd5\u76f4\u63a5\u4e0b\u8f7d\u7684\u9700\u8981\u81ea\u884c\u4e0b\u8f7d\u5168\u57fa\u56e0\u7ec4\u5e8f\u5217\u548cgtf\u6587\u4ef6\uff0c\u6839\u636e cellranger mkref\u6784\u5efa\u53c2\u8003\u6570\u636e\u5e93 wget ftp:\/\/ftp.ensembl.org\/pub\/release-97\/fasta\/danio_rerio\/dna\/Danio_rerio.GRCz11.dna.primary_assembly.fa.gz gunzip Danio_rerio.GRCz11.dna.primary_assembly.fa.gz wget ftp:\/\/ftp.ensembl.org\/pub\/release-97\/gtf\/danio_rerio\/Danio_rerio.GRCz11.97.gtf.gz gunzip Danio_rerio.GRCz11.97.gtf.gz cellranger mkgtf Danio_rerio.GRCz11.97.gtf Danio_rerio.GRCz11.97.filtered.gtf –attribute=gene_biotype:protein_coding \\ –attribute=gene_biotype:lincRNA \\ –attribute=gene_biotype:antisense \\ –attribute=gene_biotype:IG_LV_gene \\ –attribute=gene_biotype:IG_V_gene \\ –attribute=gene_biotype:IG_V_pseudogene \\ –attribute=gene_biotype:IG_D_gene \\ –attribute=gene_biotype:IG_J_gene \\ –attribute=gene_biotype:IG_J_pseudogene \\ –attribute=gene_biotype:IG_C_gene \\ –attribute=gene_biotype:IG_C_pseudogene \\ –attribute=gene_biotype:TR_V_gene \\ –attribute=gene_biotype:TR_V_pseudogene \\ –attribute=gene_biotype:TR_D_gene \\ –attribute=gene_biotype:TR_J_gene \\ –attribute=gene_biotype:TR_J_pseudogene \\ –attribute=gene_biotype:TR_C_gene cellranger mkref –nthreads=80 –genome=ref_zebr_GRCz11 –fasta=Danio_rerio.GRCz11.dna.primary_assembly.fa –genes=Danio_rerio.GRCz11.97.filtered.gtf –ref-version=3.1.0 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/421"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=421"}],"version-history":[{"count":6,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/421\/revisions"}],"predecessor-version":[{"id":433,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/421\/revisions\/433"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=421"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=421"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=421"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}