问题 采用RSeQC 对bam 文件进行质控分析时，用inner_distance.py报错。

...tie_merged.bed  -o UHR_inner_size Traceback (most recent call last):   File "/usr/local/bin/inner_distance.py", line 4, in <module>     import pkg_resources   File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 2749, in <module>     working_set = WorkingSet._build_...

文章 An introduction to PERMANOVA and ANOSIM

PERMANOVA（Permutational Multivariate Analysis of Variance）和 ANOSIM（Analysis of Similarities）都是用于分析和比较群组间多元数据差异的统计方法。它们特别适用于生态和环境科学领域，但也可应用于其他需要分析复杂数据集的科学研究。这两...

文章 flowCore R包安装报错

...                                         ^~~~~~~~ In file included from /share/work/biosoft/gcc/gcc-v6.4.0/include/c++/6.4.0/memory:81:0,                  from /share/work/biosoft/R/R-v4.2.0/lib64/R/library/RProtoBufLib/include/google/protobuf/stubs/common.h:41,   ...

问题 GEOquery 下载不了数据

...gt; workdir = "H:/gene_family/GEO数据挖掘/GES66597" >  > if( !file.exists(workdir) ){ +   if( !dir.create(workdir, showWarnings = FALSE, recursive = TRUE) ){ +     stop(paste("dir.create failed: workdir=",workdir,sep="")) +   } + } > #设置工作路径 > setwd(workdi...

文章 如何计算基因组中的连锁不平衡

...用plink软件进行： #将vcf文件转换成plink格式plink --vcf yourfile.vcf --recode --out yourfile --allow-extra-chr#计算位点之间的r2#--ld-window-kb 250 对距离在250kb之内的SNP位点进行分析（默认为1Mb）#--ld-window-r2 0.2  仅输出r2高于该参数值的LD分析结...

问题 No such file or directory at script/get_fa_by_id.pl line 23.老师，请问这个脚本的问题有什么办法解决。前几个脚本都没问题。我把脚本换了个文件还是不行。

文章 univariate_cox_batch.r 基因表达量批量单因素cox回归分析

...ata, --metadata metadata                        input metadata file path with suvival time [required]  -g expset, --expset expset                        input gene expression set file [required]  -t time, --time time  set suvival time column name in metadata [default    ...

问题 没有发现CA凭证等。 “could not read CA certificate “C:\Users\username\.docker\machine\machines\default\ca.pem”: open C:\Users\yqiu29.docker\machine\machines\default\ca.pem: The system cannot find the file specified.”

没有发现CA凭证等。 “could not read CA certificate “C:\Users\username\.docker\machine\machines\default\ca.pem”: open C:\Users\yqiu29.docker\machine\machines\default\ca.pem: The system cannot find the file specified.”

文章 seqkit序列处理神器的常用命令

...            real time recursive concatenation and streaming of fastx filesseq             转换序列(反向，补充，提取ID…)shuffle         随机序列sliding         序列滑窗提取，支持环形基因组sort            按id/名称/序列/长度排序序...

问题 CombineGVCFs报错：htsjdk.samtools.SAMFormatException: Did not inflate expected amount

...reads=4" --use-jdk-inflater true --use-jdk-deflater true --reference /path/to/part.fasta $(for i in {001..300}; do echo "--variant /path/to/part_gvcf/${i}.g.vcf.gz " ;done) --intervals chr2_part1 --output /path/to/part_gvcf/chr2_part1.g.vcf.gz --tmp-dir /path/to/temp，其中“--use-jdk-inflater tr...

问题 你好，我安装gwas的镜像报错failed to register layer: ApplyLayer exit status 1 stdout: stderr: lchown /biosoft/emmax-beta-07Mar2010: invalid argument。docker是最新版本10.14，安装其他镜像如转录组的和重测序的都没有问题 。

文章 vcf过滤时GATK和bcftools的index报错及解决方式

...解决过程： gatk报错  An index is required but was not found for file drivingVariantFile 这个报错是因为GATK读别的软件生成的vcf.gz文件，需要一个索引 所以使用bcftools建立索引 bcftools index -t filter1.vcf.gz#-t 建立tbi索引 但此时bcftools又报错  i...

问题 TCGA数据生存时间怎么确定？

... "icd_o_3_site"                                "icd_o_3_histology"                            [9] "icd_10"                                      "tissue_prospective_collection_indicator"     [11] "tissue_retrospective_collection_indicator"   "d...

文章 植物嫁接砧木影响接穗代谢通路，激素等等总结

One hypothesis is that rootstock-induced vigour may be caused by signals such as water, nutrients, and especially hormones and nucleic acids that move through the graft union to affect scion growth. In support of this hypothesis, a significant number of mobile macromolecules can move through the vas...

文章 indel vcf文件转化为SNPT输入文件

...e List::Util qw(shuffle);use Data::Dumper;use FindBin qw($Bin $Script);use File::Basename qw(basename dirname);use Cwd qw(abs_path);my $version="1.0.0";my $BEGIN_TIME=time();my @Original_ARGV=@ARGV;# ==============================================================# Get Options# =======================...