Question: MCScanX result problem
0
gravatar for HZZ0036
19 months 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 • 1.7k views
ADD COMMENTlink modified 4 months ago by nareshmvr0 • written 19 months ago by HZZ00360
0
gravatar for kashiff007
19 months ago by
kashiff00750
Cologne
kashiff00750 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 19 months ago by kashiff00750

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 19 months 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 19 months ago by kashiff00750

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 19 months ago by HZZ00360

what command you have used for blastall?

ADD REPLYlink written 19 months ago by kashiff00750

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 19 months ago by HZZ00360

remove this: -num_alignments 5

ADD REPLYlink written 19 months ago by kashiff00750

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 19 months 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 18 months ago by HZZ00360

Hi, I run into the same problem, how do you solve it? Thanks in advance

ADD REPLYlink written 12 months ago by liufeibio0

whats the solution? facing the same problem.

ADD REPLYlink written 7 months ago by 1234anjalianjali123430

Hii Anjali,

Did you find solution for this issue. Can you please help me to fix this.

ADD REPLYlink written 4 months ago by nareshmvr0

can you share your files so that we can go through them to know the problem?

ADD REPLYlink written 4 months ago by 1234anjalianjali123430

Hii

I am also struggling with same problem. Can you help me out how to fix this issue. I tried checking blast file and gff file ids . All are same. So please help me with your experience to fix this.

ADD REPLYlink written 4 months ago by nareshmvr0

Hi! I used SyMAP instead of MCScan.

ADD REPLYlink written 4 months ago by HZZ00360
0
gravatar for nareshmvr
4 months ago by
nareshmvr0
nareshmvr0 wrote:

Hii Liu,

I am struggling with same issue. If you fixed it please can you help me to sort this out.

ADD COMMENTlink written 4 months ago by nareshmvr0
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