找到约 15 条结果

文章 简单的数据处理代码

... executes the abundance summarization on the input file based on the group information in the map file.')    ex_parser.add_argument("-i", "--input_file", help="Sub-item abundance file with format specified above", required=True)    ex_parser.add_argument("-m", "--map_file", help="Map file contai...

问题 变异结果质控过滤,去掉低质量变异结果时报错i

...entry: ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles"> Warning: Expected at least 2 parts in FORMAT entry: ID=...

文章 tassel 软件做GWAS关联分析多年多点表型数据整理格式

...-trait-format Trait Format This format does not require users to provide information on number of rows and columns. The file starts with the key word <Trait> followed by names of columns. The column for line should not be labeled and elements are tab delimited. Example 1, Simple list of tra...

文章 TCGA临床数据各列含义

...prior to treatment. clinical_stage Stage group determined from clinical information on the tumor (T), regional node (N) and metastases (M) and by grouping cases with similar prognosis for cancer. colorectal_cancer Text term to signify whether a patient has been diagnosed with colorectal ...

文章 基因组注释分析方法

...n models were finally functionally annotated by integrating the annotation information from InterProScan (v5.18-57.0)79, the NCBI nonredundant protein database (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) and the eggNOG database (v5.0) (http://eggnog5.embl.de/#/app/downloads).  Shen, Y., Li, W., Zeng, Y...

问题 蛋白三维结构预测遇到问题:当在swiss-model中选择使用模板的方法时,在上传模板的时候发现因为以下问题没法上传

... must occur in ascending order. That way, the structure does not apply for modelling 个人感觉是PDB文件是不是出现不标准,残基的排序有问题,需要重新排序,这样的话,应该怎么弄 Chains A, B of the uploaded template do not start with residue no. 1. Will be renum...

问题 RNAseq有参转录组分析差异表达分析这一环节出现一些问题,ggplot版本问题

...lot2 3.4.0. ℹ Please use `linewidth` instead.  3: In DESeqDataSet(se, design = design, ignoreRank) :   some variables in design formula are characters, converting to factors 4: Removed 116 rows containing missing values or values outside the scale range (`geom_point()`).  5: Removed 116 ro...

问题 WGCNA官网处理大量基因的方法

表达矩阵有60000多个基因,在Network construction and module detection部分采用官网给的脚本,哪一步有moduleLabels?与课程给的代码怎么衔接上

文章 vif.cca 筛选环境变量:VIF是非常有用的指示符,表明数据集中存在多重共线性。 它不能很好地指示应从模型中删除哪个预测变量。

...ighly correlated with other predictors, it contains little or no unique information, and there is redundancy in the set of predictors.We don’t really want to have redundant predictors in a constrained ordination: they make the analysis more difficult to interpret, and the more predictors we hav...

文章 ssgsea_enrich_diff.r GSVA富集分析

... expression file path[required] -m META, --meta META Input the clinical information file path that contains the grouping[required] -n GROUP_NAME, --group_name GROUP_NAME Specifies the column name that contains grouping info...

问题 UPARSE to pick OTUs in QIIME

 I have some confusion about the OTU picking methods "usearch"  and "usearch61" in QIIME (pick_otus.py command). Do they use the same algorithm as UCLUST in otu picking, exept the function of low abundance clusters filter and chimera detection in "usearch"  and "usearch61"?  And what is more, wh...

文章 Rocks reinstall on compute node, after disk rebuild, fails

...: [ date ] [ thread ] [ subject ] [ author ] I think on key tidbit of information would help you here. You only run insert-ethers when you are trying to install a NEW appliance (e.g. compute node). If you just want to re-install an existing node, you do not use insert-ethers. Insert-ethers i...

文章 samtools使用

... recalculate MD/NM tags and '=' bases fixmate fix mate information reheader replace BAM header targetcut cut fosmid regions (for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates -- File operations coll...

问题 tassel 运行报错 The fixed effect design matrix has less than full column rank. The analysis will not be run.

代码如下: run_pipeline.pl -fork1 -h all.hmp -fork2 -r trait.txt  -fork3 -q population_structure.txt -fork4 -k kinship.txt -combine5 -input1 -input2 -input3 -intersect -combine6 -input5 -input4 -mlm -export mlmkq -runfork1 -runfork2 -runfork3 -runfork4 运行后:

文章 微生物互作网络构建教程网站--Microbial association network construction tutorial

...多样,下面给大家推荐一个网站,Microbial association network construction tutorial (打开链接可以点这里),列举了多种常用互作关系分析的方法(如下图)。 点击对应的分析方法,就可以看到比较细致的分析步骤了,当然,也可下...