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bhofmei / jbplugin-methylation

JBrowse plugin for methylation related things
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A error at #14

Closed Treywea closed 6 years ago

Treywea commented 6 years ago

Hi there,

When I try this plugin into my JBrowse, I find an error that: there is not a mC recover at - strand of some position, but after I run the default python script(allc_to_bigwig_pe_v3.py) to generate bw files. Then the files added more position in.

For example:

in my allc files there is not a mC recover at Chr01, pos: 43841093 However after I run the python script and make the bw to JBrwose, there is a mC tracks at Chr01,pos: 43841093??

Would you mind help me with this issue?

Thanks!

bhofmei commented 6 years ago

Of course I can help! Can you send me a few rows of the allc file (just to double check the columns), preferably the rows around where extra positions are being added? Additionally, add the -keep option when running the script, which will save the intermediate bedGraph files. In the sequence context which the position is being added, can you send a few rows before/after this extra position?

Treywea commented 6 years ago

Thanks for you reply. I solved this problem after I sorted the allc file and redo the JBrowse.

I am not sure what is wrong during the process, but I use the same comment to generate the bw files for JBrowse.

On 21 June 2018 at 23:25, Brigitte Hofmeister notifications@github.com wrote:

Of course I can help! Can you send me a few rows of the allc file (just to double check the columns), preferably the rows around where extra positions are being added? Additionally, add the -keep option when running the script, which will save the intermediate bedGraph files. In the sequence context which the position is being added, can you send a few rows before/after this extra position?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bhofmei/jbplugin-methylation/issues/14#issuecomment-399143526, or mute the thread https://github.com/notifications/unsubscribe-auth/AF7t0sd8oSynWkOOCIqFkxg_YsHoAxFKks5t-7rzgaJpZM4UxkGv .

-- WANG QIANWEN G06A, Run Run Shaw Building, CUHK Shatin, Hong Kong Tel: (+852) 54042329

bhofmei commented 6 years ago

Hmmm that’s weird. It normally won’t produce a bw file if it isn’t sorted. I’m glad it’s working though.

On Jun 22, 2018, at 5:41 AM, Treywea notifications@github.com wrote:

Thanks for you reply. I solved this problem after I sorted the allc file and redo the JBrowse.

I am not sure what is wrong during the process, but I use the same comment to generate the bw files for JBrowse.

On 21 June 2018 at 23:25, Brigitte Hofmeister notifications@github.com wrote:

Of course I can help! Can you send me a few rows of the allc file (just to double check the columns), preferably the rows around where extra positions are being added? Additionally, add the -keep option when running the script, which will save the intermediate bedGraph files. In the sequence context which the position is being added, can you send a few rows before/after this extra position?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bhofmei/jbplugin-methylation/issues/14#issuecomment-399143526, or mute the thread https://github.com/notifications/unsubscribe-auth/AF7t0sd8oSynWkOOCIqFkxg_YsHoAxFKks5t-7rzgaJpZM4UxkGv .

-- WANG QIANWEN G06A, Run Run Shaw Building, CUHK Shatin, Hong Kong Tel: (+852) 54042329 — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bhofmei/jbplugin-methylation/issues/14#issuecomment-399386052, or mute the thread https://github.com/notifications/unsubscribe-auth/APWCOu-WU6NoE8A18xLQSpbroAG97BTrks5t_LvXgaJpZM4UxkGv.