Question: MCScanX result problem
0
gravatar for HZZ0036
10 weeks ago by
HZZ00360
HZZ00360 wrote:

Hello,

I want to use MCScanX to see the synteny blocks for my weed draft genome and maize genome. I downloaded maize genome from NCBI. Then I prepared .blast and .gff file and run ./MCScanX according to the manual, however, in the collinearity result file, it showed:

############### 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: 0.00
# Number of all genes: 1
##########################################

Besides, there is no .tandem file and html is empty. Does anybody can tell me the reason about this? Thanks.

Zhang

sequence genome • 280 views
ADD COMMENTlink modified 10 weeks ago by kashifalikhan00740 • written 10 weeks ago by HZZ00360
0
gravatar for kashifalikhan007
10 weeks ago by
Cologne
kashifalikhan00740 wrote:

Can you check your gff and blast.output file? The chr name should be same in both. And the blast.output should contain weed-weed, weed-maize, maize-weed and maize-maize while your gff should have weed the maize.

ADD COMMENTlink written 10 weeks ago by kashifalikhan00740

My draft genome has no chr name, only scaffold name. I creat a link for .blast and .gff files. Could you please have a look? Thanks. https://filemover.auburn.edu/files/files/1505337598_goosemaize.blast https://filemover.auburn.edu/files/files/1505337635_goosemaize.gff

ADD REPLYlink written 10 weeks ago by HZZ00360

As you can see, you have ".t1" is present with gene name in blast output file, but not in gff file. Either remove it from blast output or add to gff file.

ADD REPLYlink written 10 weeks ago by kashifalikhan00740

I have removed it from blast output. Now the gene name in gff file and blast output file is same, but it still doesn't work. Could you please have a look again? Here is the link:

https://filemover.auburn.edu/files/files/1505917638_goosemaize.blast https://filemover.auburn.edu/files/files/1505917678_goosemaize.gff

Thank you so much!

ADD REPLYlink written 9 weeks ago by HZZ00360

what command you have used for blastall?

ADD REPLYlink written 9 weeks ago by kashifalikhan00740

Here is the script for blastall: blastp -db /mcScanX/goose_maize -query /mcScanX/goose_maize.fa -out /mcScanX/goose_maize.blast -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5

ADD REPLYlink written 9 weeks ago by HZZ00360

remove this: -num_alignments 5

ADD REPLYlink written 8 weeks ago by kashifalikhan00740

Thanks. I have tried, but it still doesn't work. The log file showed:

Reading BLAST file and pre-processing
Generating BLAST list
0 matches imported (7239387 discarded)
0 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to /mcScanX_gg_maize_analysis/goose_maize.collinearity [29.246 seconds elapsed]
Writing multiple syntenic blocks to HTML files
mz1 GRMZM5G884466 301344228 301363304^M.html
Done! [0.706 seconds elapsed]
ADD REPLYlink written 8 weeks ago by HZZ00360

Hi,

I have solved this problem, but I got a very strange circle. Could you please see the new post: Very strange circle from MCScanX

Thanks.

ADD REPLYlink written 7 weeks ago by HZZ00360
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