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gaoyubang / nanom6A

MIT License
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Could you provide the your trained model file? #3

Closed q1134269149 closed 3 years ago

q1134269149 commented 3 years ago

Hi, I plan to use the trained model of nanom6A to predict my data directly, however, I can not find the traned model file in nanom6A or the extracted features of modified and unmodified data which used to train model. Can you provide your have trained model file in order to I can used to predict m6A sites of my data directly? Thank you! hqin

gaoyubang commented 3 years ago

download nanom6A_2021_2_6.tar.gz from https://drive.google.com/drive/folders/1Dodt6uJC7lBihSNgT3Mexzpl_uqBagu0?usp=sharing, the example scripts is run_source_code.sh. you can find what you want.

q1134269149 commented 3 years ago

Thank you for your prompt reply. When I ran predict_sites, I got an error : "please check your genome file index, make shure you index with samtools index and picard CreateSequenceDictionary !". However, I have make the reference.fa.fai index with "samtool faidx reference.fa" and the picard CreateSequenceDictionary with "java -jar picard.jar CreateSequenceDictionary R=reference.fa O=reference.fa.dict". The ref folder has contained reference.fa, reference.fa.fai and reference.fa.dict. Could you give me some advice? Thanks. hqin

gaoyubang commented 3 years ago

please rename reference.fa.dict to reference.dict

q1134269149 commented 3 years ago

I still get the same error after rename.

gaoyubang commented 3 years ago

I run the test file, it runs without warning. you can also insert python scripts print(faidx1,faidx2) in predict_sites.py 512 line; these will tell us, what is wrong

q1134269149 commented 3 years ago

Thanks, I read your code, and I found that reference files and output files were not in the same folder which caused this error. hqin

q1134269149 commented 3 years ago

I suggest that you can update your code to add the input path that is same as reference.fa to the faidx1 and faidx2. Or prompt the user to place all files containing reference.fa, reference.dict and reference.fa.fai in the same directory in the description document. Thanks hqin

gaoyubang commented 3 years ago

Thank you for your suggestion, i will do it later.

q1134269149 commented 3 years ago

Thanks

gaoyubang commented 3 years ago

The module is in the nanom6A_x_x_x.tar.gz file, which can be downloaded from https://drive.google.com/drive/folders/1Dodt6uJC7lBihSNgT3Mexzpl_uqBagu0?usp=sharing.