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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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Blast+ blastn, No data in output file #72

Open Rktf opened 8 months ago

Rktf commented 8 months ago

Good day,

For MCScanX, is it Ok to use blast+ blast nucleotide (blastn) instead of blastall? I'm using bellow command : blastn -query xxx.fasta -subject zzz.fasta -evalue 1e-10 -num_threads 40 -max_target_seqs 5 -outfmt 8 -out xyz.blast

Then, I get no data inside the .collinearity output file after running MCScanX command. So I don't know if blastn is the reason or what else.

.collinearity output file :

############### Parameters ###############

MATCH_SCORE: 50

MATCH_SIZE: 5

GAP_PENALTY: -1

OVERLAP_WINDOW: 5

E_VALUE: 1e-05

MAX GAPS: 25

############### Statistics ###############

Number of collinear genes: 0, Percentage: -nan

Number of all genes: 0

########################################## ~ ~ ~ ~

Warm regards

kamalmdmostafa commented 3 months ago

I hope you have found a solution by now. Here is what might work for you: Even though the recommendation is to use blastp or diamond blast, blastn will also work as long as it is in m8 format. The trick is, after compiling the MCScanX, you should copy and chmod +x MCScanX inside the folder where you have your blastn/blastp and gff/bed format (chr gid start end), then run ./MCScanX with the prefix of your off and blast. For example, if your gff file is named xyz.gff and your blast file is named xyz.blast, you would run ./MCScanX xyz. Let me know if it worked or not.