low kernal density for a species pair

[karthickbrlab]

Hi, in the attached file the kernel density of a species pair is very low.

how to interpret the wgdi analysis.

Did the analysis correct

[SunPengChuan]

Are you referring to the blue-purple curve? I think it's fine. The reason why it's so flat may be that there are many short blocks. I suggest you limit the length of the blocks, for example, longer than 10. The curve may not be so flat, but the peak value should remain unchanged.

[karthickbrlab]

Hi.. Thanks for your reply.. I have changed the block_length option in KsPeaks and PeakFit..But it doesn't work. Where should I change this block length parameter? regards karthick

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On Thu, Aug 22, 2024 at 5:49 PM sunpengchuan ***@***.***> wrote: Are you referring to the blue-purple curve? I think it's fine. The reason why it's so flat may be that there are many short blocks. I suggest you limit the length of the blocks, for example, longer than 10. The curve may not be so flat, but the peak value should remain unchanged. — Reply to this email directly, view it on GitHub <#52 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBQ4H4YTVWRWOGOXDARFS7LZSXJOLAVCNFSM6AAAAABM54H7JKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBUGUZTCMBSGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[SunPengChuan]

You can use the -c parameter to configure the settings. However, since I can't see your settings, I'm unable to solve the issue for you.

[karthickbrlab]

Got it..Thank you.. One more query, WGDI tool will be good if the genome of interest is at contig level.. Or should all the analysed genome need to be chromosome level?.

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On Sun, 25 Aug, 2024, 12:52 am sunpengchuan, ***@***.***> wrote: You can use the -c parameter to configure the settings. However, since I can't see your settings, I'm unable to solve the issue for you. — Reply to this email directly, view it on GitHub <#52 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBQ4H46L4TC4LORB2R555MDZTDMQJAVCNFSM6AAAAABM54H7JKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBYGUYDMNJQGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[SunPengChuan]

WGDI can analyze genomic data at the contig level. Contigs with fewer than 5 genes are typically too short to extract meaningful collinearity and should be removed from the lens file.