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Published 20 hours ago • verified publisher icon tanghaibao

Can I use jcvi to plot the MCSCanX

Open wuxiaopei0509 opened this issue 4 years ago • 6 comments

Hi ,Mr Tang I use MCSCanX to find collinearity blocks and found about 1000 blocks between two species ,However When I use the jcvi only 523 blocks in the Jcvi. My question is Can I use the MCScanX results to plot the Synteny between the two species ? Thank you

wuxiaopei0509 avatar May 14 '20 11:05 wuxiaopei0509

@wuxiaopei0509

The default filtering criteria (BLAST filters to remove weak and tandem duplicates) are different between MCScanX and jcvi version. The default synteny block threshold is also different. That's why the numbers are different. However, both should be fine to use as long as you keep track of the parameters that were used.

To plot MCscan results, you need to convert the MCScanX output to .anchors format. What is .anchors format? See discussion here.

Haibao

tanghaibao avatar Jun 13 '20 03:06 tanghaibao

Could you please show in code how to convert the MCScanX output (.collinearity) to .anchors format?

ShuaiNIEgithub avatar Sep 28 '20 08:09 ShuaiNIEgithub

@ShuaiNIEgithub

Sorry for the late response but you could try:

python -m jcvi.compara.synteny fromaligns mc.collinearity

Let me know if this doesn't work and also send me a small file for testing.

tanghaibao avatar Dec 22 '20 06:12 tanghaibao

@tanghaibao It worked and that's what I wanted. Thank you very much for your reply!

ShuaiNIEgithub avatar Dec 25 '20 07:12 ShuaiNIEgithub

Hi @tanghaibao, Rather than open a new issue i thought this was more appropriately posted here, as this is where my googling led me.

I wish to play with my macrosynteny plots in SynVisio. Is there a way to convert an anchors file into a collinearity file? Or would I have to install and runMCScanX to generate this?

Many thanks, really liking the software so far

mrmrwinter avatar Aug 05 '22 13:08 mrmrwinter

@mrmrwinter

Unfortunately, we don't yet have a conversion script as you said at this point. If you do figure out how to do it, please consider contributing this. I think other ppl have asked about this in the past.

Haibao

tanghaibao avatar Aug 05 '22 14:08 tanghaibao

Hi mrmrwinter, Have you solved this problem. I also need to tansfer anchor files generated by JCVI to collinearity files generated by MCScanX, which could used by SynVisio.

dengyang111 avatar Jun 08 '23 09:06 dengyang111

I can not plot the synteny graph. The script gave me an error when I try to do it. It said that the chromosomes are empty. Could it be a problem with the seqid or layout files? outmcscan.err.txt

mpodio81 avatar Nov 01 '23 16:11 mpodio81