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MCScanX result problem

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

genome sequence
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updated by pmcarlton • pmcarlton • written by HZZ0036 • HZZ0036

2 answers

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.

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written by kashiff007 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.

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written by kashiff007 kashiff007

what command you have used for blastall?

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written by kashiff007 kashiff007

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

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written by HZZ0036 • HZZ0036

remove this: -num_alignments 5

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written by kashiff007 kashiff007

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]
• 0 views • link
written by HZZ0036 • HZZ0036

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

• 0 views • link
written by pmcarlton • pmcarlton

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

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written by liufeibio • liufeibio

Hii Anjali,

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

• 1 views • link
written by nareshmvr • nareshmvr

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

• 1 views • link
written by 1234anjalianjali1234 • 1234anjalianjali1234

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.

• 1 views • link
written by nareshmvr • nareshmvr

Hi! I used SyMAP instead of MCScan.

• 1 views • link
written by HZZ0036 • HZZ0036

Hii Liu,

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

• 1 views • link
written by nareshmvr • nareshmvr

Did you find a way ?

• 0 views • link
written by venura venura

No

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在 2019年10月23日，下午7:25，venura on Biostar <mailer@biostars.org<a rel="nofollow" href="mailto:mailer@biostars.org">mailer@biostars.org> 写道：

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

Did you find a way ?

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written by HZZ0036 • HZZ0036

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

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written by wangqingtianxie • wangqingtianxie

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