找到约 15 条结果

文章 Git基本命令

...set --hard HEAD^ 丢弃工作区的修改（撤销）： git checkout -- file 删除文件: 正确操作：git rm file git commit -m “remove file”（文件被删除）操作失误：git checkout -- file（文件被恢复）https://blog.csdn.net/csdnnews/article/details/78849117

问题 进行16S分析时，对样品按照分组进行分类汇总出现问题。

...absolute.$i -a -L 2,3,4,5,6,7> doneTraceback (most recent call last):  File "/share/work/biosoft/python/Python2/bin/collapse_samples.py", line 93, in                                                                                                  ...

文章 安装R包出现链接库缺失的问题

...h/00new/igraph/libs/igraph.so':  libglpk.so.36: cannot open shared object file: No such file or directory 如上面的报错,这个时候最简单的办法是通过locate查看是否存在链接库(linux里) locate libglpk.so/usr/local/lib/libglpk.so/usr/local/lib/libglpk.so.36/usr/local/lib/libg...

问题 鲁棒性检验代码

...e, status=status, x=n, method="efron", max.n.genes=20, n.iter=10, n.seq=1) Please wait...Error in model.frame.default(formula = Surv(time, status) ~ x[, i]) :   变数的长度不一样('x[, i]')> fit$model错误: 找不到对象'fit'

文章 MUMmer + SVMU : CNVs

...10 < svmu.cmds.sh#SVMU 结果说明：# sv.prefix.txt = A tab delimited file that summarizes structural mutations (indels, CNVs, inversions) in the sample genome with respect to the reference genome.  # # small.prefix.txt: A tab delimited file containing SNPs and small indels that occur within...

文章 maf_oncoplot.r突变注释文件分类可视化maftools

...ncoplot.r -h usage: /share/nas1/zhangll/MAF/code/maf_oncoplot.r [-h] -i maffile -m metadata -g group [-a additive [additive ...]] [-T topgene] ...

文章 Python学习-利用Python对植物基因组注释文件（gff3格式）进行处理

...息 #!usr/bin/python import re,io from operator import itemgetter input_file = io.open('Zmays_284_Ensembl-18_2010-01-MaizeSequence.gene.gff3','r',encoding='UTF-8') # 基因的注释信息,GFF3格式的文件 out_file = open('Zm.newid.gff', 'w', encoding='UTF-8') # 输出文件的名字 list_two = [...

文章 trinity的下载与安装

...quantifygraph这一步  –output trinity的输出文件夹 –no_version_check 不汇报版本信息 注：trinity支持分步骤运行，但我认为必要性不大，因为分步运行的原因在于避免中途发生错误，但是trinity会自动检测之前输入，如果中途发生报错...

文章 MFP - Molecular Functional Portrait

...nature_scores_scaled.to_csv('signature_scores.tsv', sep='\t', index=True)# Check the clustering within a range of 30 to 65% similarity.# >65% - usually graph is not connected; <30% - unreasonable correlationclustering_metrics = clustering_profile_metrics(signature_scores_scaled, threshold_mm=(...

问题 在运行table_annovar.pl脚本的时候报错

...l_sample_INS_DEL.avinput> NOTICE: Finished reading 6401 lines from VCF file NOTICE: A total of 6371 locus in VCF file passed QC threshold, representing 0 SNPs (0 transitions and 0 transversions) and 6371 indels/substitutions NOTICE: Finished writing allele frequencies based on 0 SNP genotypes ...

问题 bam文件排序时出错

... "main" htsjdk.samtools.util.RuntimeIOException: Problem writing temporary file file:///work/my_reseq/tmp/sortingcollection.2676215835069172723.tmp.  Try setting TMP_DIR to a file system with lots of space.         at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:26...

文章 R magick 包安装包错

...: dotplot -> <Anonymous> 查了下需要升级R包：clusterProfiler等等 但是升级不成功：说magick安装不上，这里报错： Error: package or namespace load failed for ‘magick’ in dyn.load(file, DLLpath = DLLpath, ...):  unable to load shared object '/share/work/...

文章 iTOL进化树外层添加圆环

... data below (TAB,SPACE or COMMA).This separator must be used throught this file (except in the SEPARATOR line, which uses space).#SEPARATOR TABSEPARATOR SPACE#SEPARATOR COMMA#label is used in the legend table (can be changed later)DATASET_LABEL color_strip2#dataset color (can be changed later)COLOR ...

文章 GFF或GTF格式转bed

...软件安装 $ git clone https://github.com/bedops/bedops.git$ cd bedops$ make$ make install GFF格式转bed gff2bed <gencode.v19.annotation.gff3 > test.bedconvert2bed -i gff -o bed <gencode.v19.annotation.gff3 > test.bed GTF格式转bed gtf2bed <gencode.v19.annotation.gtf > t...

问题 老师好，我在做群里遗传进化算pca时，得到的文件都是0。但是没有报错

...ary.bim +plink_pca-temporary.fam written.2045265 variants loaded from .bim file.2045265 missing IDs set.684 people (0 males, 0 females, 684 ambiguous) loaded from .fam.Ambiguous sex IDs written to plink_pca.nosex .Using up to 23 threads (change this with --threads).Before main variant filters, 684 f...