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darelab2014 / Dinopore

DInoPORE: Direct detection of INOsines in native RNA with nanoPORE sequencing
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Missing groundtruth classification file #1

Closed matthewstuartedwards closed 2 years ago

matthewstuartedwards commented 2 years ago

Hi, the usage of the program requires a -c argument with the ground truth classification. The example for running mainscript1.sh shows

-c /data/xen_s9_r1_50k/groundtruth_classification.txt

I haven't been able to find this file anywhere, including in the CloudOcean capsule. Can you provide this file?

darelab2014 commented 2 years ago

Hi @matthewstuartedwards, I have removed all the data from GitHub to save the cloning time. You can file "data" folder, including all files you need in our CodeOcean https://doi.org/10.24433/CO.2180901.v1 Let me know if you have any other questions. Cheers, NTA

darelab2014 commented 2 years ago

Hi, my lab told me that the file is in CodeOcean. Can you check again? Thanks!

Best Regards Meng How

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From: matthewstuartedwards @.> Sent: Tuesday, 21 June 2022 1:25 am To: darelab2014/Dinopore @.> Cc: Subscribed @.***> Subject: [darelab2014/Dinopore] Missing groundtruth classification file (Issue #1)

Hi, the usage of the program requires a -c argument with the ground truth classification. The example for running mainscript1.sh shows

-c /data/xen_s9_r1_50k/groundtruth_classification.txt

I haven't been able to find this file anywhere, including in the CloudOcean capsule. Can you provide this file?

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darelab2014 commented 2 years ago

Hi @matthewstuartedwards, sorry for the inconvenience, "-c /data/xen_s9_r1_50k/groundtruth_classification.txt" is just for example, in CodeOcean, the groundtruth file is /data/xen_s9_r1_50k/groundtruth_class_regression.tsv. I have updated the README file to reflect this. Thank you for letting us know. Cheers, NTA

matthewstuartedwards commented 2 years ago

Thanks, I thought that .tsv file was probably the right file, but thought if anything this issue would get the README updated.