地址:https://gitlab.com/leoisl/dbgwas 下载(自测):https://www.dropbox.com/s/s9oojqfl1kgi4l5/DBGWAS-0.5.4-Linux-precompiled.tar.gz?dl=1 使用方法 ## 01.run-dbgwas.Rdrug="meropenem"meta=read.csv2("./input/meta-data.csv")#---## prepare dbgwas config file ##---## specify str...
We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k-mer-...
第三步(学习步骤:最终被视为要包含在最终抗生素中的候选特征预测模型):将每个已识别的集群总结为一个新的复合变量,定义为定义集群的原始变量的平均值,并在集群级别执行标准套索。因为在我们的案例中,原始变量编码基因组中给定DBGWAS模式的存在/不存在,这些复合变量对应于基因组中存在/不存在的集群中涉及的模式比例。
42]. Moreover, the SLE GWAS SNPs were enriched in SPI1 ChIP-seq (Fig. S11) and the top GWAS SNPs for SLE corresponded to a known SPI1 motif. These results suggest that the ΔMOCCS2score can be used to predict the cell types in which GWAS-SNPs potentially influence TF-binding specific...
地址:https://gitlab.com/leoisl/dbgwas#compiling 1 git下载,source安装default GCC 4.8.2+ cmake v3.6+ make zlib 1.2.11+ git # 两个问题 # 1 gcc gcc -v # 版本低 export PATH=/route/.conda/envs/bioenv/bin:$PATH # 一次性,也可添加到.bashrc最后,每次使用source即可 gcc -v g++ -v # ...
A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy a
Genome-wide association studies (GWAS) have allowed the discovery of marker鈥搕rait associations in crops over recent decades. However, their power is hampered by a number of limitations, with the key one among them being an overreliance on single-nucleotide polymorphisms (SNPs) as ...
In this study, we performed a k-mer-based genome-wide association study (GWAS) in 98 A. fumigatus isolates from public databases. Associations identified with k-mers not only recapitulate those with SNPs but also discover new associations with insertion/deletion (indel). Compared to SNP sites,...