Dispersed bin squares in Saddle plots for individual chromosomes

[yermek2030]

Many thanks for creating such a fantastic tool!
1). I have been successfully building AB enrichment profiles for individual chromosomes with 20 bins, 'uncentered', the 10 bin plots 'uncentered' are also good. However, when I try to plot 10 (Figure1), 20 (Figure2), or 100 bins 'centered' (Figure3) my bin squares appear disjointed from each other. In fact, at 100 bin resolution, even the uncentered bins look dispersed (Figure4) with large white gaps between them. The only difference between Figure 3 and Figure 4 (centered and uncentered respectively) is that the bin cubes are slightly larger in uncentered.
Is it related to coverage (but mine is higher than 30x) or the specificity of FAN-C?
2). Also, when I do 'uncentered' option at any number of bins, the resolution drops to half of the number of bins I have specified for some reason: for example, if I put 10 bins the plot comes out with 5 bins (5x5 square). So, below on the centered plots you can see 20 and 40 bins despite me specifying 10 and 20 bins respectively (Figure 1 and Figure 2)
Thanks.

[kaukrise]

Hey, I'm currently on holiday, so can only look at this in a few weeks, sorry

[kaukrise]

Hey, sorry about the delay. Can you please send me the complete commands that you used, from generating the AB enrichment matrix to plotting the saddle plot? Thank you!

[yermek2030]

Hi, no problem. Can I send it to you as a private message somehow here?

[yermek2030]

fanc compartments -g myzdisk/0_genomes/mm39/mm39.fa -v CTKOwt_norm_2Mb.corrected.chr19.ev.txt CTKOwt_norm_2Mb.corrected.chr19.cool CTKOwt_norm_2Mb.corrected.chr19.ab -f -x chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chrX chrY chrY_JH584303v1_random --recalculate #Doing uncentered, because centered causes problems: fanc compartments -g myzdisk/0_genomes/mm39/mm39.fa -d CTKOwt_norm_2Mb.corrected.chr19.domains_gc.bed -e CTKOwt_norm_2Mb.corrected.chr19.ab_profile_uncentered_20bin.png CTKOwt_norm_2Mb.corrected.chr19.cool CTKOwt_norm_2Mb.corrected.chr19.ab --compartment-strength CTKOwt_norm_2Mb.corrected.chr19.comp_strength.txt -f -x chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chrX chrY chrY_JH584303v1_random -p 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 #Regardless of whether it is centered or uncentered - white lines are produced fanc compartments -g myzdisk/0_genomes/mm39/mm39.fa -d CTKOwt_norm_2Mb.corrected.chr19.domains_gc.bed -e CTKOwt_norm_2Mb.corrected.chr19.ab_profile.png CTKOwt_norm_2Mb.corrected.chr19.cool CTKOwt_norm_2Mb.corrected.chr19.ab --compartment-strength CTKOwt_norm_2Mb.corrected.chr19.comp_strength.txt -p 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 -f -x chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chrX chrY chrY_JH584303v1_random -s 0 fanc compartments -g myzdisk/0_genomes/mm39/mm39.fa -d CTKOwt_norm_2Mb.corrected.chr19.domains_gc.bed -e CTKOwt_norm_2Mb.corrected.chr19.ab_profile_centered_20bin.png CTKOwt_norm_2Mb.corrected.chr19.cool CTKOwt_norm_2Mb.corrected.chr19.ab --compartment-strength CTKOwt_norm_2Mb.corrected.chr19.comp_strength.txt -f -x chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chrX chrY chrY_JH584303v1_random -p 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 -s 0 #White cross is formed fanc compartments -g myzdisk/0_genomes/mm39/mm39.fa -d CTKOwt_norm_2Mb.corrected.chr19.domains_gc.bed -e CTKOwt_norm_2Mb.corrected.chr19.ab_profile_centered_10bin.png CTKOwt_norm_2Mb.corrected.chr19.cool CTKOwt_norm_2Mb.corrected.chr19.ab --compartment-strength CTKOwt_norm_2Mb.corrected.chr19.comp_strength.txt -f -x chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chrX chrY chrY_JH584303v1_random -p 10 20 30 40 50 60 70 80 90 100 -s 0 fanc compartments -g myzdisk/0_genomes/mm39/mm39.fa -d CTKOwt_norm_2Mb.corrected.chr19.domains_gc.bed -e CTKOwt_norm_2Mb.corrected.chr19.ab_profile_uncentered_20bin.png CTKOwt_norm_2Mb.corrected.chr19.cool CTKOwt_norm_2Mb.corrected.chr19.ab --compartment-strength CTKOwt_norm_2Mb.corrected.chr19.comp_strength.txt -f -x chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chrX chrY chrY_JH584303v1_random -p 10 20 30 40 50 60 70 80 90 100 2023 ж. 17 там., бс, 18:01 күні kaukrise ***@***.***> жазды:

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Hey, sorry about the delay. Can you please send me the complete commands that you used, from generating the AB enrichment matrix to plotting the saddle plot? Thank you! — Reply to this email directly, view it on GitHub <#162 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJC3RG3B7RXD3TICQZ36DM3XVYBZBANCNFSM6AAAAAA2UFZ36M> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[kaukrise]

Thank you. Your chosen resolution is simply far too large for the fine-grained percentiles you've chosen. Try something smaller, like 100kb. The reason that this is more pronounced when using centred saddle plots is because 0 is chosen as the midpoint, and if the EV has more negative than positive values (or vice versa) this will affect the side with less values.

[yermek2030]

I see. Thanks for explaining! 2023 ж. 17 там., бс, 18:46 күні kaukrise ***@***.***> жазды:

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Thank you. Your chosen resolution is simply far too large for the fine-grained percentiles you've chosen. Try something smaller, like 100kb. The reason that this is more pronounced when using centred saddle plots is because 0 is chosen as the midpoint, and if the EV has more negative than positive values (or vice versa) this will affect the side with less values. — Reply to this email directly, view it on GitHub <#162 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJC3RGYPEBT43MM5WLRYTG3XVYHAVANCNFSM6AAAAAA2UFZ36M> . You are receiving this because you authored the thread.Message ID: ***@***.***>