找到约 15 条结果

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

...2 on chrB6+, this line 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...

文章 GSDS网站docker镜像本地构建

...            0omicsclass/sratoolkit          SRAtoolkit v2.10.3 and aspera v3.9.9.177872     0omicsclass/ampliseq-q2         Amplicon sequencing qiime2 v2020.2 image        0omicsclass/bsaseq              NGS Bulk Segregant Analysis image               0omicsclas...

文章 提取miRNA前后500bp序列

...                       <int>        Other parameter:-h           Help documentUsage End.exit;} my $len = $opts{l}; $len ||=500;my $in  = Bio::SeqIO->new(-file => "$opts{fa}" , -format => 'Fasta');my %fasta;while ( my $seq = $in->next_seq() ) {my...

文章 IF=4.8 | 不同菊花品种萜类合成相关基因的转录组代谢组联合分析

... BMC Plant Biology杂志发表了一篇题为“Integrative transcriptome and metabolome analysis reveals candidate genes related to terpene synthesis in Chrysanthemum × morifolium”的转录组代谢组联合分析文章。” 01 — 研究背景 菊花（Chrysanthemum × morifolium）是...

文章 6分SCI（医学类）-按这个思路很好发！

...可见cg13652336, cg25123470和cg06038133为风险因子，而cg05254747 and cg04907664为保护因子。 模型性能评估 为了评估预后预测模型的性能，以预测模型在数据集上预测值的中位值为阀值将样本分成高风险和低风险两组，两组样本采用KM分...

问题 docker运行qiime1时按照教程进行到章节2课时6时，即聚类生成OTU-denovo时老是报错，查看类似问题后，升级了运行内存为70g，同时将教程内的30多个样本减成2个样本，FASTQ格式还有qimme格式检查都正确，依旧报错，报错内容如下：

...ckages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.   warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') Traceback (most recent call last):   File "/biosoft/miniconda/envs/qii...

文章 vcf过滤时GATK和bcftools的index报错及解决方式

...-t filter1.vcf.gz#-t 建立tbi索引 但此时bcftools又报错  index: the file is not BGZF compressed, cannot index 这是因为bcftools只能对bgzip压缩后的文件建立索引，而上面使用的压缩方式是gzip 解决方式： 对文件解压之后重新用bgzip压缩，再建立...

文章 泌尿感染（UTIs）宏基因组分析

... Wallace MA, Burnham CD, Dantas G. Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Microbiome. 2022 Jan 17;10(1):6. doi: 10.1186/s40168-021-01204-9. PMID: 35039079; PMCID: PMC8762997.

问题 docker运行qiime1时按照教程进行到章节2课时6时，即聚类生成OTU-denovo时老是报错，查看类似问题后，升级了运行内存为70g，同时将教程内的30多个样本减成2个样本，FASTQ格式还有qimme格式检查都正确，依旧报错，报错内容如下：Segmentation fault

...ckages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.   warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') Traceback (most recent call last):   File "/biosoft/miniconda/envs/qii...

文章 封装型分面facet_wrap()

...~ 4        20    28 p    # ... with 224 more rows, and 1 more variable: class <chr>> P <-  ggplot(mpg,aes(x = cty, y = hwy)) + geom_point()+ facet_wrap( ~ cyl + drv, nrow = 2 )> print(P) 基于cly 和drv 两列变量进行分面 生...

文章 qiime2 couldn't connect to display "localhost:12.0"

...ite-packages/qiime2/sdk/action.py", line 245, in bound_callable output_types, provenance) File "/share/work/biosoft/conda/Miniconda3.8/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 452, in _callable_executor_ ret_val = self._callable(output_dir=temp_dir, **view...

文章 多基因间共线性及局部基因水平的共线性

... Tcacao_233_cds.fa.gz cacao.cds $ python -m jcvi.formats.gff bed --type=mRNA --key=Name Tcacao_233_gene.gff3.gz -o cacao.bed 2.共线性搜索 $ python -m jcvi.compara.catalog ortholog peach cacao --cscore=.99$ python -m jcvi.compara.synteny screen --minspan=30 --simple p...

文章 SCP 安装成功的单细胞转录组 docker镜像使用 single-cell-v5

...ration_method = "Seurat")CellDimPlot(  srt = panc8_sub, group.by = c("celltype", "tech"), reduction = "SeuratUMAP2D",  title = "Seurat", theme_use = "theme_blank")panc8_rename <- RenameFeatures(  srt = panc8_sub,  newnames = make.unique(capitalize(rownames(panc8_sub[["RNA"]]), force_tolower =...

文章 如何将ENSEMBL ID转换成Gene ID(ENTREZID)或者Symbol

...YMBOL"), keytype="ENSEMBL")'select()' returned 1:many mapping between keys and columns> dim(list)[1] 29140 3> head(list,5) ENSEMBL ENTREZID SYMBOL1 ENSG00000121410 1 A1BG2 ENSG00000175899 2 A2M3 ENSG00000256069 3 A2MP14 ENSG00000171428 9 NAT15 E...

文章 投稿时-SCI期刊文章中图片大小如何设置

... 原文地址：https://www.elsevier.com/authors/author-schemas/artwork-and-media-instructions/artwork-sizing TARGET SIZEImage widthPixels at 300 dpiPixels at 500 dpiPixels at 1000 dpiMinimal size30 mm (85 pt)3545911181Single column90 mm (255 pt)1063177235431.5 column140 mm (397 pt)16542756551...