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文章 tcga_gene_exp_download.r TCGA数据下载脚本使用说明。

使用方法： usage: tcga_gene_exp_download.r [-h] -p project [-f files.per.chunk]                                [-o outdir]TCGA 基因表达数据下载及临床数据下载与整理，详细帮助见:https://www.omicsclass.com/article/1485optional arguments:  -h, --help    ...

文章 rockes7 共享目录设置

...户端的使用者用户统一被转换成匿名用户nfsnobody。subtree_check （默认）  若输出目录是一个子目录，则nfs服务器将检查其父目录的权限。no_subtree_check  即使输出目录是一个子目录，nfs服务器也不检查其父目录的权限，这样可以提...

文章 openssl 安装

... ./config --prefix=/usr/local/ssl --openssldir=/usr/local/ssl shared zlib make && make install 代码语言：javascript复制#修改软连接 ln -s /usr/local/ssl/bin/openssl /usr/bin/openssl ln -s /usr/local/ssl/include/openssl /usr/include/openssl 更新：/lib64/libssl* /lib64/libcryp...

文章 简单的数据处理代码

...     args = self.args        probe_expr_df = pd.read_csv(args.input_file, sep="\t", header=0, index_col=0)        probe_expr_df.index = probe_expr_df.index.map(str)        # Normalize expression data        abundances = [self.norm_expr(probe_expr_df, norm_type) for norm_type in arg...

文章 根据fastq ID列表，输出指定ID对应的双端或单端fastq文件

... import gzipimport argparsedef extract_gene_names(input_fastq_gz, output_file):    with gzip.open(input_fastq_gz, 'rt') as fastq_gz, open(output_file, 'w') as out_file:        line_count = 0        for line in fastq_gz:            line_count += 1            if line_count % 4 =...

问题 合并gvcf的问题

... <NON_REF> as an allele but that is not the case at position 763769; please use the Haplotype Caller with gVCF output to generate appropriate records。由于缺乏bam文件我只能尝试别的方法合并，当使用bcftools时提示：X602.g.vcf.gz was expected to contain a single sample bu...

问题 下载COAD数据提示列不一致保存不成功

... GDCdownload(query = query, +             directory = DataDirectory,files.per.chunk=6, method='client') Downloading data for project TCGA-COAD Of the 521 files for download 521 already exist. All samples have been already downloaded > # 保存结果 > data <- GDCprepare(query = ...

文章 immune_compare_stat.r 免疫细胞表达差异比较

...t.r  -husage: /work/STAD_immu_demo1/scripts/immune_compare_stat.r [-h] -i filepath -v                                                           celltype                                                           [celltype ...] -m       ...

问题 tassel报错，[Thread-9] ERROR net.maizegenetics.plugindef.AbstractPlugin - 0，软件运行有些表型数据时无问题，但大部分表型数据运行时出现该错误

...bstractPlugin -  FixedEffectLMPlugin Parameters phenoOnly: false saveToFile: false siteFile: null alleleFile: null maxP: 1.0 permute: false nperm: 0 genotypeComponent: Genotype minClassSize: 0 biallelicOnly: false siteStatsOut: false siteStatFile: null appendAddDom: false [Thread-9...

问题 使用xpclr分析出现TypeError: ufunc 'true_divide' not supported for the input types'

...022-06-24 16:17:52 : INFO : 73,412 SNPs in total are in the provided input files 2022-06-24 16:17:52 : INFO : 0 SNPs excluded as multiallelic 2022-06-24 16:17:52 : INFO : 0 SNPs excluded as missing in all samples in a population 2022-06-24 16:17:52 : INFO : 22,496 SNPs excluded as invariant or si...

问题 用linux系统做gwas时运行脚本报错[Thread-9] ERROR net.maizegenetics.plugindef.AbstractPlugin - 0

...sselPipeline - parseArgs: NOTE: The -glm flags are deprecated. parseArgs: PLEASE RUN THIS COMMAND TO GET USAGE: ./run_pipeline.pl -FixedEffectLMPlugin [Thread-9] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.IntersectionAlignmentPlugin: time: Nov 30, 2023 17:14...

问题 xpclr报错AttributeError: 'NoneType' object has no attribute 'keys'

...lling back to scanning to region') Traceback (most recent call last):   File "/hpc/home/t2024096/.conda/envs/xpclr/bin/xpclr", line 196, in <module>     main()   File "/hpc/home/t2024096/.conda/envs/xpclr/bin/xpclr", line 97, in main     g1, g2, positions, genetic_dist = xpclr.util....

文章 seurat_sc_cluster.r 使用帮助：

...t scripts/seurat_sc_cluster.r -husage: scripts/seurat_sc_cluster.r [-h] -i filepath [-d dim]                                   [--resolution resolution [resolution ...]]                                   [--umap.method umap.method]                      ...

文章 TCGA临床数据下载—TCGAbiolinks

...: indexed clinical: a refined clinical data that is created using the XML files.XML files: original source of the dataBCR Biotab: tsv files parsed from XML files There are two main differences between the indexed clinical and XML files: XML has more information: radiation, drugs information, foll...

问题 动植物基因组组装课程，结构注释部分，运行braker.pl出错

...es 系统提示： Failed  to create new species with new_species.pl, check write permissions in /share/work/biosoft/augustus/latest/config//species directory!     Command was perl /share/work/biosoft/augustus/augustus-3.3.3/scripts/new_species.pl --species=Acer_truncatum --AUGUSTUS_CONFIG_P...