MCScanX result problem

Question

[HZZ0036]

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

Answer 1

[kashiff007]

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.

[HZZ0036]

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

[kashiff007]

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.

[HZZ0036]

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!

[kashiff007]

what command you have used for blastall?

[HZZ0036]

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

[kashiff007]

remove this: -num_alignments 5

[HZZ0036]

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]

[pmcarlton]

I solved this by making sure that both the .blast and the .gff files were TAB-delimited. I had the same "0 matches imported" problem when the .gff file was space-delimited.

The tr command can be used to change it easily:

```bash < file.gff tr ' ' '\t' > file_tab.gff

[HZZ0036]

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.

[liufeibio]

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

[1234anjalianjali1234]

whats the solution? facing the same problem.

[nareshmvr]

Hii Anjali,

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

[1234anjalianjali1234]

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

[nareshmvr]

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.

[HZZ0036]

Hi! I used SyMAP instead of MCScan.

Answer 2

[nareshmvr]

Hii Liu,

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

[venura]

Did you find a way ?

[HZZ0036]

No

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在 2019年10月23日，下午7:25，venura on Biostar <[e-mail]<a rel="nofollow" href="mailto:[e-mail]">[e-mail]> 写道：

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User venuravenura wrote Comment: MCScanX result problemC: MCScanX result problem:

Did you find a way ?

[wangqingtianxie]

"Solution is to put .blast and .gff file inside MCScanX folder without creating a separate folder." it woreked!