siduanmiao
commented
1 week ago Thank you very much for your feedback. We have optimized the code. Regarding your questions, here are our responses:
- /home/sirm/graduation_design/snakemake_folder/Demo_data/ATAC/fragment_file and others are just comments we wrote during the code development process. You don't need to remove or modify them.
- The missing files have been embedded in the code. You can re-clone our repository and rerun the process, and you should not encounter this issue again.
- Yes, you only need to run this script to obtain the results after data processing.
1、对于/scripts/ATAC/ATAC_DAP.R文件里最上方的
path = '/home/sirm/graduation_design/snakemake_folder/Demo_data/ATAC/fragment_file'
species = 'Hs'
这两个变量的设置是否需要去掉注释，并换成自己的。 （另外在ATAC的其他代码文件里，也出现以上的变量设置的注释，应该怎么处理） 另外按照readme的文件中提到： Demo_data ├── RNA │ ├── raw.h5ad │
│
├── ATAC ├── fragment.tsv.gz ├── fragment.tsv.gz.tbi ├── cbc_perturbation_dict.tsv
以上的文件组织形式，ATAC里并没有fragment_file文件，如果要换成自己的，应该改成什么合适 （我下载了demo数据，并把其中的如上对应的四个文件拿出来，构成以上格式）
2、缺失文件
运行 bash RNA_all.sh /path_to_your_file/Demo_data/RNA Hs 之后，发现缺失文件 FileNotFoundError: [Errno 2] No such file or directory: '/home/wzt/database/ENSEMBL2SYMBOL_Hs.tsv'
在/scripts/RNA/myUtul.py文件里，存在对这一文件的读取 def transID(adata, species): adata.var_names_make_unique() adata.obs_names_make_unique() if species == 'Mus musculus': dat = pd.read_csv('/home/wzt/database/ENSEMBL2SYMBOL_Mm.tsv', sep='\t') else: dat = pd.read_csv('/home/wzt/database/ENSEMBL2SYMBOL_Hs.tsv', sep='\t')
但这个文件未提供
3、得到数据处理后的结果是否只需要运行以下脚本就可以得到数据处理后的结果 bash ATAC_fragment_all.sh /path_to_your_file/Demo_data/ATAC Hs bash RNA_all.sh /path_to_your_file/Demo_data/RNA Hs
期待您的解答！感谢！