How to generate xyz.blast file for MCScanX using the target nuclotide sequences and genome ?

[xinkwu]

Hi, Yupeng

I have successfully installed MCScanX. The xyz.blast file was generated by command blastall -i sim.cluster.fasta -d DSim_pilon.fasta -p blastn -e 1e-10 -b 5 -v 5 -m 8 -a 15 -o xyz.blast

The DSim_pilon.fasta was the database generated by command formatdb -i DSim_pilon.fasta -p F

The gff file like this tig00000001|arrow|pilon tig00000001|arrow|pilon:3569293-3582540(-) 3569293 3582540 tig00002065|arrow|pilon tig00002065|arrow|pilon:11837-22762(-) 11837 22762

but after running command< MCScanX xyz>, there was no alignment result in xyz.collinearity file and the html file was also wrong.

What mistake did I take when I was generating the .blast file? Thank you so much!

Kai

[xinkwu]

the head of xyz.blast file I generated before

tig00001719|arrow|pilon:11858-35596(+) tig00001719|arrow|pilon 100.00 9759 0 0 2619 12377 14477 24235 0.0 1.892e+04 tig00001719|arrow|pilon:11858-35596(+) tig00001719|arrow|pilon 100.00 3018 0 0 14771 17788 26629 29646 0.0 5834 tig00001719|arrow|pilon:11858-35596(+) tig00001719|arrow|pilon 100.00 2573 0 0 1 2573 11859 14431 0.0 5011

[xinkwu]

Or MCScanX can only handle blastp output ?