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kadenerlab / cORF_pipeline

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what is the format of annotation file? #1

Open zhanghao-njmu opened 6 years ago

zhanghao-njmu commented 6 years ago

Dir sir: I cannot run the script because I don't know the format of the annotation file required. As far as i know, this not a standard bed format. Which format do i need to send to the parameter? Best wish!

kadenerlab commented 6 years ago

You can see the format of the annotation file in the example " annotation_example_dm3.txt https://github.com/kadenerlab/cORF_pipeline/blob/master/annotation_example_dm3.txt" in the github.

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On Sat, Jan 6, 2018 at 6:36 PM, zh542370159 notifications@github.com wrote:

Dir sir: I cannot run the script because I don't know the format of the annotation file required. As far as i know, this not a standard bed format. Which format do i need to send to the parameter? Best wish!

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blueheavan commented 4 years ago

Dir sir: I cannot run the script because I don't know the format of the annotation file required. As far as i know, this not a standard bed format. Which format do i need to send to the parameter? Best wish!

Dear Sir, I have the same problem. May you help me, please.

kadenerlab commented 4 years ago

You have test files in the pipeline folder. Please use them to see the exact formst.

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בתאריך יום ב׳, 10 בפבר׳ 2020, 17:23, מאת blueheavan ‏< notifications@github.com>:

Dir sir: I cannot run the script because I don't know the format of the annotation file required. As far as i know, this not a standard bed format. Which format do i need to send to the parameter? Best wish!

Dear Sir, I have the same problem. May you help me, please.

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zhuyiqin commented 2 years ago

the test annotation file has no descriptions for each column, so I don't know how to make my own annotation file.

sumu-ai commented 2 years ago

Dear Sir, It's not clear what each column represents in annotation file in the example,especially the last few columns Best wish!

DooYal commented 3 months ago

the test annotation file has no descriptions for each column, so I don't know how to make my own annotation file.

The format of annotation file is called genepred, which can be transfered by https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred