DiTing
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xuechunxu
DiTing: A pipeline to infer and compare biogeochemical pathways in metagenomic data
共组装
你好，请问当我样本有4个平行的时候， sample_one_1.fastq sample_one_2.fastq sample_two_1.fastq sample_two_2.fastq sample_three_1.fastq sample_three_2.fastq sample_four_1.fastq sample_four_2.fastq 但是我是通过共组装得到的，想使用这个共组装得到的assembly，应该如何选择参数，谢谢你
Dear all Given that DiTing requires paired end fastq reads as input, is there a way one can use the tool with Nanopore fastq reads? Thanks Marcus
Hi there, I have been attempting to run DiTing on some metatranscriptome and metagenome datasets, however I am getting an error I do not understand. I have installed DiTing and...
Hello Thanks for the exceptional contribution of the pipelines I'm trying prove my own cycle of catabolism, It's possible do it? and how? . Thanks for your advice....
Run error
Dear Sir or Madam, I followed your installation recommondations but I am unable to run DiTing on the example read data. with: diting.py -r /ext/DiTing/example -o Clean-reads_interleaved.diting.out I get the...
Hi Xuechun, could you please implement a `--continue` option to avoid recomputation for failed jobs? It seems the current version will simply overwrite everything, it would be great to have...
as above, i hava a predicted table related KEGG genes, how could i calculate the gene family using scripts pathway.py?
User input: /home/meta/mdisk/pl/earthworm/fastq/VFDB_database/kofam_database/DiTing-master/diting.py -r /home/meta/mdisk/pl/soil/test_diting -o /home/meta/mdisk/pl/soil/test_diting/out -n 30 -a /home/meta/mdisk/pl/soil/test_diting/fasta 2024-07-16 14:52:32 [INFO ] **************[1/12] Check database*************** 2024-07-16 14:52:32 [INFO ] The KEGG database is set 2024-07-16 14:52:32 [INFO...
For sulfate reduction, the siroheme-dependent anaerobic sulfite reductase (asr) genes, and octaheme cytochrome c sulfite reductase (mccA) would be a good addition to the sulfite to sulfide step to ensure...
Hello, Thank you very much for such a cool pipeline. I used it for MAGs using this suggestion https://github.com/xuechunxu/DiTing/issues/9#issuecomment-997932469. But renaming the MAGs according to the fastq file works when...
