找到约 15 条结果

问题 重测序

...就可以运行，在sh里面怎么说找不到文件那。命令如下 for i in $(cat $workdir/data/data.txt); do echo "RUN CMD: fastp --thread 50 --qualified_quality_phred 10 \    --unqualified_percent_limit 50 \    --n_base_limit 10 \    -i $datadir/${i}_1.fastq.gz \    -I $datadir/$...

问题 用linux系统做gwas时运行脚本报错[Thread-9] ERROR net.maizegenetics.plugindef.AbstractPlugin - 0

...fault: false) -siteFile <Statistics File> : The name of the file to which these results will be saved. -alleleFile <Genotype Effect File> : The name of the file to which these results will be saved. -maxP <max P value> : Only results with p <= maxPvalue will be reported. Defa...

问题 安装 velocyto 报错

...dor/pyproject_hooks/_in_process/_in_process.py", line 132, in get_requires_for_build_editable           return hook(config_settings)         File "/tmp/pip-build-env-fyxtx39r/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 448, in get_requires_for_build_editable   ...

问题 TCGAbiolinks包

你好，我遇到了跟你一样的问题Downloading genome information (try:0) Using: Human genes (GRCh38.p13) 错误: $ operator is invalid for atomic vectors 请问怎么更新R包解决呢？

问题 建立索引时报错，有很多关于mRNA的错误输出文件为部分为0KB

...e is on chrB6-, all group members must be on same seq and strand RUN CMD: retrieve_seq_from_fasta.pl --format refGene --seqfile elepant_grass_genome.fa  unknown_refGene.txt --out unknown_refGeneMrna.fa NOTICE: Reading region file unknown_refGene.txt ... Done with 4143 regions from 1 chromosomes ...

问题 GEO数据库下载的表达矩阵转换成genesymbol时报错。perl脚本。请问perl脚本的问题出在哪？需要怎么修改。最后有perl及需要处理的数据的百度云链接（链接：https://pan.baidu.com/s/1fKim1pGNsU4DDJXcxchplg 提取码：5ls1）

...my @samp1e=(localtime(time)); if($.==1) { my @expArr=split(/\t/,$exp); for(my $i=0;$i<=$#expArr;$i++) { my $singleName=$expArr[$i]; $singleName=~s/\"//g; if($i==0) { push(@sampleName,"ID_REF"); } else { my @singleArr=split(/\_|\./,$singleName); push(@sampleName,$singleArr[0]); } ...

问题 GEO数据库下载的表达矩阵转换成genesymbol时报错。perl脚本。请问perl脚本的问题出在哪？需要怎么修改。最后有perl及需要处理的数据的百度云链接（链接：https://pan.baidu.com/s/1fKim1pGNsU4DDJXcxchplg 提取码：5ls1）

...p($exp);my @samp1e=(localtime(time));if($.==1){my @expArr=split(/\t/,$exp);for(my $i=0;$i<=$#expArr;$i++){my $singleName=$expArr[$i];$singleName=~s/\"//g;if($i==0){push(@sampleName,"ID_REF");}else{my @singleArr=split(/\_|\./,$singleName);push(@sampleName,$singleArr[0]);}}}else{my @expArr=split(/\...

文章 Repeat masking in MAKER2 (difference with BRAKER2)

1.9.1 Repeat masking in MAKER2 (difference with BRAKER2) For repeat masking, MAKER2 used the same repeat libraries (generated by RepeatModeler) as BRAKER2 (for details, see section 1.4.2 about repeat masking). It is important to note that even though MAKER2 and BRAKER2 used the same repeat libra...

问题 cc1plus: error: unrecognized command line option "-std=gnu++11"

...std=gnu++11" make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘later’ * removing ‘/share/work/biosoft/R/R-v3.6.1/lib64/R/library/later’ ERROR: dependency ‘later’ is not available for package ‘promises’ * removing ‘/share/work/biosoft/R/R-v3.6.1/lib64/R/l...

问题 利用GATK 分染色体call 变异时出现错误

我用如下命令：  for i in $(cat $workdir/data/data.txt) ; do  for Chr in Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12; do   echo "gatk --java-options "-Xmx100g" HaplotypeCaller \     -R $REF \     -I $workdir/3.map/result/${i}.sorted.dedup.bam \   ...

文章 bedtools统计序列中碱基含量

...number of times a user-defined sequence                        is observed (case-sensitive).        -C      Ignore case when matching -pattern. By defaulty, case matters.        -fullHeader     Use full fasta header.                - By default, only the word before ...

问题 最新qiime2教程16S注释报错

...ics/pairwise.py:1776: DataConversionWarning: Data was converted to boolean for metric jaccard   warnings.warn(msg, DataConversionWarning) /biosoft/miniconda/envs/ampliseq-q2/lib/python3.8/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py:143: RuntimeWarning: The result contai...

文章 perl 中批量创建不同的文件，用于文件批量分隔成小文件

...建文件，把创建的文件句柄放到，hash中存储； my%fout=();for my$i (1..10){my $f=FileHandle->new("> ${i}_links.txt");$fout{$i}=$f;} #根据不同的条件输出到不同的文件当中 while(<IN>){my@tmp=split(/\t/);print $fout{$tmp[0]}  $_;}

文章 串联重复基因 tandem和segmental的区别与联系

...Holub [1], a chromosomal region within 200 kb containing two or more genes is defined as a tandem duplication event. 3.染色体片段复制(Segmental duplication)：导致复制的基因距离较远，甚至位于不同的染色体。 总结：基因家族串联复制与加倍定义 Segmenta...

文章 ppi_network.r 蛋白互作网络分析

... identifiers of the organism (e.g. 9606                        for Human, 10090 for mouse). default 9606  -t score_threshold, --score_threshold score_threshold                        a threshold for the combined scores of the                        interactions, ...