找到约 15 条结果

文章 bedtools批量提取基因组指定位置序列

...asta> -bed <bed/gff/vcf>Options:        -fi     Input FASTA file        -bed    BED/GFF/VCF file of ranges to extract from -fi        -name   Use the name field for the FASTA header        -split  given BED12 fmt., extract and concatenate the sequencesfrom the BED "blo...

文章 lasso_cox.r lasso_cox 模型优化分析

... show this help message and exit -i data, --data data input data file path[required] -t time, --time time set suvival time column name [required] -e event, --event event set event column name [required] -v variate [variate ...], --variate variate [variate ......

文章 easySFS的使用

...是运行preview，确定每个群体向下投影的值。 easySFS.py -i file.vcf -p pop.txt --preview > proj_flag proj_flag文件的主要内容如下： Pop1 (2, 45.0) (3, 59.0) (4, 58.0) (5, 49.0) (6, 41.0) (7, 35.0) (8, 27.0) (9, 20.0) (10, 13.0) (11, 8.0) (12, 8.0) ...

文章 deepseek绘图之--微生物堆叠柱状图

...")# 读取数据otu_table <- read.delim("otu_table.txt", row.names = 1, check.names = FALSE)tax_table <- read.delim("tax_table.txt", row.names = 1)sample_table <- read.delim("sample_table.txt", row.names = 1)# 数据处理流程（先过滤低丰度物种，再计算相对丰度）plot_data...

问题 devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")运行错误

...方案运行了代码 结果一直报错，显示Error in utils::download.file(url, path, method = download_method(), quiet = quiet,  :    cannot open URL 'https://api.github.com/repos/BioinformaticsFMRP/TCGAbiolinks/tarball/master'  有没有大神能帮忙看看是个什么情况啊

文章 At core/community/optimal_modularity.c:87 : GLPK is not available, Unimplemented function call

...Source/amd_preprocess.o AMD/Source/amd_valid.o AMD/Source/amdbar.o CHOLMOD/Check/cholmod_check.o CHOLMOD/Check/cholmod_read.o CHOLMOD/Check/cholmod_write.o CHOLMOD/Cholesky/cholmod_amd.o CHOLMOD/Cholesky/cholmod_analyze.o CHOLMOD/Cholesky/cholmod_colamd.o CHOLMOD/Cholesky/cholmod_etree.o CHOLMOD/Cho...

文章 sed使用

...： -e script: 允许直接在命令行中提供编辑脚本。-f script-file: 从指定的文件中读取编辑脚本。-n: 仅打印经过sed处理的行，而不打印原始文件中的未修改行。-i: 直接修改文件内容，而不是输出到标准输出（屏幕）。通常与模式字...

文章 GATK外显子测序数据肿瘤体细胞突变数据分析

...apiens_assembly38.fasta \ -V 154.raw.somatic.vcf.gz  -O  154.filter.checked.vcf.gz &&\ zcat 154.filter.checked.vcf.gz |awk '$0~/#/ || ($7 =="PASS"){print $0}' |bgzip  >154.clean.vcf.gz && rm -f 154.filter.checked.vcf.gz 3.对突变结果进行注释 使用...

文章 TGS-gapcloser 安装与使用

...map2ln -s MINIMAP2所在文件夹 TGS-GapCloser/ 编译 cd TGS-GapCloser/make 编译时出现问题： 解决： cd ./common/time# 在timetools.h文件前面加上#include <ctime>vi timetools.h# 退回TGS-GapCloser/cd ../../make 2.使用 采用之前组装的fa文件对现在...

文章 Perl 包和模块

...行以上程序将输出： Writing Person/lib/Person.pm Writing Person/Makefile.PL Writing Person/README Writing Person/t/Person.t Writing Person/ChangesWritingPerson/MANIFEST Person 目录下你可以看到新增加的目录及文件说明: README ：这个文件包含一些安装信息，模...

文章 单细胞转录组数据挖掘流程记录-头颈癌（HNSCC）(GSE181919)

...et -c "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE181919&format=file&file=GSE181919%5FBarcode%5Fmetadata%2Etxt%2Egz" -O GSE181919_Barcode_metadata.txt.gz wget -c "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE181919&format=file&file=GSE181919%5FUMI%5Fcounts%2Etxt%2Egz" -O ...

问题 win10家庭版安装docker desktop,运行时报错

...ine/v1.40/version: open //./pipe/docker_engine: The system cannot find the file specified. In the default daemon configuration on Windows, the docker client must be run elevated to connect. This error may also indicate that the docker daemon is not running.

问题 gatk call SNP样品多采取方法2，报错如下是怎么回事啊

A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file

问题 基因家族分析时，提取cds与pep序列报错显示 no sequence

Error, no sequence for Scaffold1 at /share/work/biosoft/TransDecoder/latest/util/gff3_file_to_proteins.pl line 84. 应该如何解决？代码与报错如下， 我的基因组gff文件是这样的，我看课程示例文件是ID=XX;Parent=xx,是因为这个才提取不出来吗

问题 R包ridge 安装报错

...ation Error: package or namespace load failed for ‘ridge’ in dyn.load(file, DLLpath = DLLpath, ...):  unable to load shared object '/share/work/biosoft/R/R-v4.0.3/lib64/R/library/00LOCK-ridge/00new/ridge/libs/ridge.so':   /share/work/biosoft/R/R-v4.0.3/lib64/R/library/00LOCK-ridge/00new/rid...