找到约 15 条结果

问题 微生物多样性分析课程镜像ampliseq-q2运行出错：there is no package called ‘BiocManager’

...da2: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more. Debug info has been saved to /tmp/qiime2-q2cli-err-u8wvbzh9.log 打开日志文件： Error in library(BiocManager, quietly = TRUE) : there is no package called ‘BiocMa...

文章 immune_box_plot.r 免疫侵润box分布图

... $ Rscript $scriptdir/immune_box_plot.r -husage: immune_box_plot.r [-h] -i filepath -m                                                       filepath -g group                                                       [-b groupby]            ...

问题 基因组注释Braker里面的报错

...enes” 报错“# Mon Aug 12 20:10:06 2024: Log information is stored in file /work/work/xsyj/genome_annotation/03.Braker/braker/braker.log ERROR in file /share/work/biosoft/BRAKER/latest/scripts//braker.pl at line 6666 Failed to execute: perl /share/work/biosoft/GeneMark-ES/latest/gmes_linux_64...

文章 如何使用 wget 下载一个目录下的所有文件

ftp://ftp.ebi.ac.uk/pub/databases/Rfam/14.1/fasta_files/ 方法如下： wget -r -np -nH -R index.html http://url/including/files/you/want/to/download/ 各个参数的含义： -r : 遍历所有子目录 -np : 不到上一层子目录去 -nH : 不要将文件保存到主机名文件夹 ...

问题 pip install RSeQC安装时候报错，是不是底层的库不全？怎么解决呢

...e output from command /usr/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-ZbI2FB/bx-python/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-iavnDe --pytho...

文章 统计不同分组差异表达结果并统计上下调基因数目并绘制柱状图

...(files,function(fl){d=read.table(fl,header=TRUE,comment.char="",sep = "\t",check.names=FALSE)[,c(1,18)]}) #将数据整理成表格mydatamydata=sapply(data,function(d){table(d[,2])})colnames(mydata)<-c("DAF2 vs GDAF2","DAF5 vs GDAF5","DAF11 vs GDAF11","DAF16 vs GDAF16")mydata=as.data.frame(melt(m...

文章 Rna-seq 去除批次效应ComBat-seq

library(sva)df=read.table("all_gene_count_raw.xls",head=T,check.names=F,comment.char="")head(df) batch=c("3D","3D","3D","7D","7D","7D","3D","3D","3D","7D","7D","7D")#group=c(0,0,0,0,0,0,1,1,1,1,1,1)df[,-c(1,13)] <- ComBat_seq(df[,-c(1,13)], batch=batch, group=NULL)write.table(df,file =...

文章 samtools之index

...t; [out.index] Options:    -b    Generate BAI-format index for BAM files[default]    samtools index -b xx.bam  建立索引后将产生后缀为.bai的文件    -c    Generate CSI-format index for BAM files    samtools index -c xx.bam  建立索引后将产生后缀为.csi...

文章 MCscan报错——kpsewhich命令缺失

...顺利，但是运行时总会报错。 MCscan报错信息：    File "/biosoft/python/Python-v2.7.11/lib/python2.7/site-packages/jcvi/graphics/dotplot.py", line 357, in dotplot_main    title=opts.title, stdpf=(not opts.nostdpf))  File "/biosoft/python/Python-v2.7.11/lib/python...

文章 如何用R语言绘制进化树+热图

...ad.tree(opt$tree) tax <- read.table(opt$tax,row.names = 1,header = TRUE,check.names = FALSE,sep = "\t") groupInfo <- split(row.names(tax),tax$phylum) tree2 <- groupOTU(tree,groupInfo) tax_p <- tax[,-1] p <- ggtree(tree2,aes(color=group),right = TRUE)+theme(legend.position= "right")+...

文章 mapman非模式植物基因注释时遇到的问题

...hway or process to be visualized. Each diagram consists of a pathway image file (.svg) and an extra protein/gene mapping file (.xml). Notice, the diagrams designed for Mercator4 (X4 ..) are not compatible to Mercator v.3.6 and vice versa.两个注释结果跟pathway的code根本不兼容。 解决...

问题 单细胞测序数据对合并后的样本进行聚类分析时报错

...n 0.5 -d 30 \  -p pbmc   -o pbmc 报错内容为：Error: cannot open file '/share/work/biosoft/R/R-v4.0.3/lib64/R/library/gridExtra/R/gridExtra. rdb': No such file or directory Execution halted Error: failed to load sRGB colorspace file Fatal error: error during cleanup 想问下老师，...

问题 blastp提示ensemble中提取的序列文件不对

...n-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options 已去除序列中的终止子符号。 e.g： >ENST00000620518 ENSG00000081692  JMJD4 1:227732392-227735273(-) MDRETRALADSHFRGLGVDVPGVGQAPGRVAFVSEPGAFSYAD...

问题 ANNOVAR变异注释报错：Erro: invalid record found in exonic_variant_function file (exonic format error)

....var_ann/test/snp.avinput> NOTICE: Finished reading 840 lines from VCF file NOTICE: A total of 224 locus in VCF file passed QC threshold, representing 224 SNPs (152 transitions and 72 transversions) and 0 indels/substitutions NOTICE: Finished writing allele frequencies based on 1344 SNP genoty...

文章 安装gdal报错

...下错误： sudo yum install gdal gdal-devel Last metadata expiration check: 3:25:35 ago on Tue 13 Jun 2023 07:28:50 AM CST.Error: Problem 1: package gdal-libs-3.4.0-2.el9.x86_64 requires libarmadillo.so.10()(64bit), but none of the providers can be installed  - package gdal-3.4.0-2.el9.x86_6...