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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
MIT License
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Mark contigs #25

Closed Li-280512 closed 2 years ago

Li-280512 commented 2 years ago

Your software is very well designed, but I have encountered some problems in using it. When I tagged contigs on the genome, I found that the color of large segments of contigs could not effectively cover the corresponding interval of the chromosome, so the size of MS needs to be adjusted, but I could not set the size accurately. Is there a way to mark this long fragment without having to resize the tag?

mnshgl0110 commented 2 years ago

I am not sure I get the issue completely. Could you please share some example? - Manish

mnshgl0110 commented 2 years ago

Your reply does not have the figures, please reupload. Also, please share the markers.bed file as well.

Li-280512 commented 2 years ago

Hi Thank you very much for your reply!! I want to mark the assembled chromosomes, which consist of several contig, I want to graph it as follows A4C602DA-C6C7-4C99-8B86-56B5B055B9C3 But when I used the --markers parameter and gave the CHR, START, END of the contig on the chromosome, the picture was as follows F52AB64A-09E1-41DD-A498-A77141880FE4 Contig doesn't actually cover the chromosomes as I gave you.I guess it's because the "ms" in the Mark file I gave is too small, but I don't know how big this parameter should be. 2E2F5624-C427-4B27-A677-4AB5998BE442

mnshgl0110 commented 2 years ago

Hi. Should be fixed with the updated version (https://github.com/schneebergerlab/plotsr/commit/bf26d9279919e7863cd016b128677942b0038d1b). Please update plotsr using the following commands and retry.

git clone https://github.com/schneebergerlab/plotsr.git
cd plotsr
python setup.py install
Li-280512 commented 2 years ago

Thank you very much for your help! I downloaded the latest plotsr==0.5.5, but when I run "plostr -h" it reported the following error, can you help me to see what the problem is. image

image

image But it was successful when I used 0.5.4

mnshgl0110 commented 2 years ago

Hi @Li-280512, sorry for the issues. Could you please re-install again? Let me know if it is still not working.

Li-280512 commented 2 years ago

Hi @mnshgl0110 Thank you for your help!!! An updated version is available. It's a really great job, thanks again. I may trouble you again if there are more questions later...