blocks mapping to the chromosome without those blocks

[123jjhy]

Dear developer, May I ask you A question about visualization, I am A different annotation(A and B) of the same genome , some blocks exist in A but not in B, there is no collinearity of both, and vice versa. Now the problem is, such blocks in A,B will show the position, but there is no collinearity, how can you make the block in A does not map to B in the corresponding position?

Thanks. target.pdf

[tanghaibao]

@123jjhy

To clarify, it looks like some of the annotations are occupying similar locations.

For example, there are genes named Pdaxxxxx vs maker-xxxxx. For a gene in question, microsynteny search will try to match the best one. Do you want to show match to both Pdaxxxx and maker-xxxxx?

One way is to manually modify the blocks file to have two lines so they both appear.

geneA  Pdaxxxxx
geneA  maker-xxxxx

[123jjhy]

@tanghaibao Thank you for your reply. What I want is that if it is not a gene pair, it is only displayed where it is present, for example, make-CHR6-snap-gene-14.25-mrNA-1, which is only present on maker Chr6, I do not want it displayed where s7 Chr6 corresponds.

------------------ 原始邮件 ------------------ 发件人: "tanghaibao/jcvi" @.>; 发送时间: 2024年4月1日(星期一) 中午12:51 @.>; @.@.>; 主题: Re: [tanghaibao/jcvi] blocks mapping to the chromosome without those blocks (Issue #639)

@123jjhy

To clarify, it looks like some of the annotations are occupying similar locations. image.png (view on web) For example, there are genes named Pdaxxxxx vs maker-xxxxx. For a gene in question, microsynteny search will try to match the best one. Do you want to show match to both Pdaxxxx and maker-xxxxx?

One way is to manually modify the blocks file to have two lines so they both appear. geneA Pdaxxxxx geneA maker-xxxxx
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[tanghaibao]

@123jjhy

Are they both called Chr6 in the bed file (first column)?

Then you need to remove make-CHR6-snap-gene-14.25-mrNA-1 from the bed file, or distinguish the two Chr6 differently - like s7_Chr6 and maker_Chr6 in the first column in the bed file. Otherwise, it will show up on the same track.

[123jjhy]

Ok, I'm thinking about it based on what you said.  I used the following two lines of command cat maker_Chr6.bed s7_117_Chr6.bed > maker_s7_Chr6.bed  python -m jcvi.graphics.synteny target.blocks maker_s7_Chr6.bed blocks.layout6

make-CHR6-snap-gene-14.25-mrNA-1 never exist in s7_117_Chr6.bed，it only existed in maker_Chr6.bed.  Thanks.

------------------ 原始邮件 ------------------ 发件人: "tanghaibao/jcvi" @.>; 发送时间: 2024年4月1日(星期一) 下午3:09 @.>; @.@.>; 主题: Re: [tanghaibao/jcvi] blocks mapping to the chromosome without those blocks (Issue #639)

@123jjhy

Are they both called Chr6 in the bed file (first column)?

Then you need to remove make-CHR6-snap-gene-14.25-mrNA-1 from the bed file, or distinguish the two Chr6 differently - like s7_Chr6 and maker_Chr6 in the first column in the bed file. Otherwise, it will show up on the same track.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>