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lulab / Ribowave

Ribo-seq data analysis tool
https://lulab.github.io/Ribowave
GNU General Public License v3.0
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ambiguous descriptions #1

Open m-swirski opened 6 years ago

m-swirski commented 6 years ago

Hi, create_track_Ribo function is described ambiguously, namely: in usage example -i options is one for .bam file, while in its usage (-h) option it is -G. Whats more -g option requires genome size and nothing like this has been created during annotation preparation. Where should I get the file? regards, Michał

lulab commented 6 years ago

Thank you for your message.

Zhiyu, Would you fix this bug? Thanks.

Sincerely, John

Zhi John Lu | 鲁 志 MOE Key Lab of Bioinformatics School of Life Sciences, Tsinghua University Beijing 100084, China http://ncrnalab.org/ http://www.ncrnalab.org/

On Thu, Aug 2, 2018 at 1:04 AM Miswi notifications@github.com wrote:

Hi, create_track_Ribo function is described ambigously, namely: in usage example -i options is one for .bam file, while in its usage (-h) option it is -G. Whats more -g option requires genome size and nothing like this has been created during annotation preparation. Where should I get the file? regards, Michał

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lulab commented 6 years ago

Thanks for your advice. The ambiguous -i,-G problem has been fixed already. And for the question about the genome size, I recommend to use samtools faidx function to calculate the size of each chromosome. We have updated the README file in the github and specially added a part referring how to generate the genome size file. I hope it would be easy to understand. Best, Zhiyu,

在 2018年8月2日，上午9:09，Zhi J. Lu (鲁志) zhilu@tsinghua.edu.cn 写道：

Thank you for your message.

Zhiyu, Would you fix this bug? Thanks.

Sincerely, John

Zhi John Lu | 鲁 志 MOE Key Lab of Bioinformatics School of Life Sciences, Tsinghua University Beijing 100084, China http://ncrnalab.org/ http://www.ncrnalab.org/

On Thu, Aug 2, 2018 at 1:04 AM Miswi <notifications@github.com mailto:notifications@github.com> wrote: Hi, create_track_Ribo function is described ambigously, namely: in usage example -i options is one for .bam file, while in its usage (-h) option it is -G. Whats more -g option requires genome size and nothing like this has been created during annotation preparation. Where should I get the file? regards, Michał

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/lulab/Ribowave/issues/1, or mute the thread https://github.com/notifications/unsubscribe-auth/AGJegqaylKvRb839cOYqLR7q6KxxTbtCks5uMd9IgaJpZM4Vq4XO.

m-swirski commented 6 years ago

Thanks, it seems to work fine now. I think the idx file for genome fasta is created automatically in your pipeline. Best, Michał