MCScanX
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wyp1125
MCscanX BLASTALL ERROR
@wyp1125 @XTan hi,i hope you will be fine.i need your help, i am new user of MCScanX.i have successfully installed MCScanX. after that i have installed ncbi-blast+.now i am confuse in "at.blast" file.my result output "at.blast" not similar with your example data "at.blast" file.kindly guide where i am wrong.i am using for "database generating" protein sequence of arabidopsis thaliana and for query sequence ,i am using same protein sequence that i was use for "database generating".if i use two genome like arabidopsis and grape,i will put arabidopsis protein sequence as a querry and for database "grape protein sequence"??kindly guide me i will be very thankful.
blast output parameter set will influence result format， check your output format about ncbi-blast @ABDULLAHGUJJAR
@jhh130910 ,after performing two genome blast i am facing problem in two genome gff file.simply i add secod genome gff file but i face the problem.can you tell me any easy way to make two genome gff file for MCscanX.
I noticed that their documentation is outdated. I've been using blastp from the blast+ v2.2.30 software package, but the output format is not 8 (as they cited in their manual), but 6.
-outfmt <String> alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1, 10 = Comma-separated values, 11 = BLAST archive format (ASN.1) 12 = JSON Seqalign output
The command I'm using is: $ blastp -outfmt 6 -query query_file.fasta -db db_name -evalue 1e-10 -max_target_seqs 5 -out output.blast -num_threads 8
I hope this helps.
Hi, @wyp1125 When I'm trying to run family_ circle_plotter I'm getting the circular plot but the collinear genes are not getting highlighted in red. I would be very grateful to you if you could suggest on this issue
