Question: MCScanX empty collinearity file.
0
gravatar for 1234anjalianjali1234
4 weeks ago by
India
1234anjalianjali123430 wrote:

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]
ADD COMMENTlink modified 8 days ago by Biostar ♦♦ 20 • written 4 weeks ago by 1234anjalianjali123430

CAN ANYONE TELL ME ABOUT THE PROCEDURE OF CLOSING THIS QUESTION?

ADD REPLYlink written 28 days ago by 1234anjalianjali123430

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?

ADD REPLYlink written 28 days ago by Philipp Bayer5.7k

Thank you for the answer.

ADD REPLYlink written 28 days ago by 1234anjalianjali123430
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