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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
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prepDE.py Error: Text file with sample ID and path invalid () #298

Open play131937 opened 4 years ago

play131937 commented 4 years ago

Hi,

I was trying to extract count matrix by prep.DE, but I was getting the error. 

Error: Text file with sample ID and path invalid ()

This is the command I used, 

$ python prepDE.py -i sample_lst_2M.txt -g ./gene_count_matrix_2M.csv -t ./transcript_count_matrix_2M.csv

This is how the sample_lst_2M.txt looks like.

Ctrl1   /home/IrisC/Hisat2/Stringtie/S0311-4h-c_L1/Ctrl1.gtf
Ctrl2   /home/IrisC/Hisat2/Stringtie/S0316-4h-c_L1/Ctrl2.gtf
2M1B1   /home/IrisC/Hisat2/Stringtie/S0311-4h-2_L1/2M1B1.gtf
2M1B2   /home/IrisC/Hisat2/Stringtie/S0316-4h-2_L1/2M1B2.gtf

The directory structure: 

$ tree -L 3 /home/IrisC/Hisat2/Stringtie/

Stringtie/
├── DE
│   └── sample_lst_2M.txt
├── S0311-4h-2_L1
│   ├── 2M1B1.gtf
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── S0311-4h-2_L1_gene_abund.tab
│   └── t_data.ctab
├── S0311-4h-c_L1
│   ├── Ctrl1.gtf
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── S0311-4h-c_L1_gene_abund.tab
│   └── t_data.ctab
├── S0316-4h-2_L1
│   ├── 2M1B2.gtf
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── S0316-4h-2_L1_gene_abund.tab
│   └── t_data.ctab
├── S0316-4h-c_L1
│   ├── Ctrl2.gtf
│   ├── e2t.ctab
│   ├── e_data.ctab
│   ├── i2t.ctab
│   ├── i_data.ctab
│   ├── S0316-4h-c_L1_gene_abund.tab
│   └── t_data.ctab
└── Read.md

I have tried executing prepDE.py by the following command but it didn't fix the error. 

$ python2.7 prepDE.py -i sample_lst_2M.txt -g ./gene_count_matrix_2M.csv -t ./transcript_count_matrix_2M.csv

Does anyone know how to fix this? Any suggestion would be appreciated.

Thanks, Iris

sumageb commented 3 years ago

Hi, I faced a similar issue. I found that there was an empty line at the bottom of the .txt file. Removing that empty line fixed my problem. You can check your txt file.

Zlingsen commented 3 years ago

Hi, I faced a similar issue. I found that there was an empty line at the bottom of the .txt file. Removing that empty line fixed my problem. You can check your txt file.

Yes, I had the same problem. Thanks very much!!!

pijush1285 commented 3 years ago

I also have same problem.