MCScanX empty collinearity file.
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3.1 years ago

Hellow,

I want to check the gene duplication of a gene within Potato genome for which I am using MCScanX.

./MCScanX data/xyz

OUTPUT is showing that there is no alingment generated:

Reading BLAST file and pre-processing
Generating BLAST list
1446 matches imported (1155 discarded)
48 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to /home/xyz.collinearity [0.389 seconds elapsed]
Tandem pairs written to /home/xyz.tandem
Writing multiple syntenic blocks to HTML files
st00.html
st1.html
st10.html
st11.html
st12.html
st2.html
st3.html
st4.html
st5.html
st6.html
st7.html
st8.html
st9.html
Done! [0.166 seconds elapsed]
MCScanX gene duplication Collinear blocks • 2.0k views
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CAN ANYONE TELL ME ABOUT THE PROCEDURE OF CLOSING THIS QUESTION?

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You should have an 'edit' button where you can delete the whole question - but to answer your question, it looks like there's something wrong with the alignments file, the tandem duplications file worked fine but the inter-species comparison is broken, perhaps because the IDs in the gff file are different than in the blast file?

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Thank you for the answer.

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6 weeks ago

How can I learn mcscanx from the scratch. Please help me by providing guidelines.

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