DiTing
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xuechunxu
DiTing: A pipeline to infer and compare biogeochemical pathways in metagenomic data
Dear developer group, Great tool, I am immensely enjoying using it, especially the cycle pathway group in the tab file. I am just wondering if it is possible to take...
您好，请教一下，为什么在pathway_relative_abundance_gene_level中carbon fixation有六条pathway(均有基因丰度），但在汇总的pathway_relative_abundance中只有四条pathway了，Hydroxypropionate-hydroxybutylate cycle和Dicarboxylate-hydroxybutyrate cycle丢失了 [pathways_relative_abundance.txt](https://github.com/xuechunxu/DiTing/files/9943794/pathways_relative_abundance.txt) [pathways_relative_abundance_gene_level.txt](https://github.com/xuechunxu/DiTing/files/9943795/pathways_relative_abundance_gene_level.txt)
Dear When I run Diting, /home/lbhuang/miniconda3/envs/diting-env/bin/diting.py -r /home/lbhuang/Moore/data/Metagenomics_test/ -o /home/lbhuang/Moore/results_test/Diting_result/ I get this erorr: 2022-09-23 20:27:50 - MEGAHIT v1.2.9 2022-09-23 20:27:50 - Using megahit_core with POPCNT and BMI2 support 2022-09-23...
你好，我按照github上的说明安装了Diting，使用时发现Check database环节，提示没有检测到KEGG数据库，然后开始了自动下载。请问可以下载到kegg数据吗？
-----Here is the wrong code----- 2022-08-19 23:41:23 [INFO ] User input: /home/miniconda3/envs/diting-env/bin/diting.py -r rawdata -o testone -n 120 **************[1/12] Check database*************** 2022-08-19 23:41:23 [INFO ] The KEGG database is set...
您好， 我在运行diting的最后生成热图时出现如下错误提示： 2022-05-26 13:56:34 [INFO ] **********[8/12] Merge KEGG annotations*********** 2022-05-26 13:56:34 [INFO ] Merge KEGG annotations 2022-05-26 13:58:06 [INFO ] [9/12] Merge KEGG annotations and gene relative abundances 2022-05-26...
I am little bit confused, what do you mean by having the dependencies installed and added to the $path, can you take one for example: like I have bbmap in...
I have metagenome samples and each sample has paired end reads as sample_R1 and sample_R2. If I use the code, diting.py -r -o . Will I get the result combinedly...
Dear authors， I have 90 samples（about 6Gbp/ sample）. When running to 7/12 step， errors occur. Could you please kindly help us to solve it? **Errors are as follows:** [7/12] KEGG...
Hi all. Is there anyway to make the taxonomy classification of some functions? For example, I would like to classify the taxonomy of nifH gene. Is there some way to...
