genes names

[MarineBergot]

Hi !

i'm using hicexplorer and i'm trying to plot HiC data with genes but something definitly wrong..

i'm using this file hic_track.ini:

[x-axis] where = top

[hic matrix] file = C1829A_LR51_50000_norm_correct.h5 title = 5kb

depth is the maximum distance plotted in bp. In Hi-C tracks

the height of the track is calculated based on the depth such

that the matrix does not look deformed

depth = 1000000 min_value = 5 max_value = 50 transform = log1p file_type = hic_matrix

[tads] file = C1829A_LR51_TADs_50000_domains.bed file_type = domains border_color = black color = none

the tads are overlay over the hic-matrix

the share-y options sets the y-axis to be shared

between the Hi-C matrix and the TADs.

overlay_previous = share-y

[Genes] file = grch38.refseq.with_genes_sorted.bed title = genes style = UCSC fontsize = 10 height=10

my grch38.refseq.with_genes_sorted.bed file looks like :

chr1 35277 35481 FAM138F chr1 35721 36081 FAM138F chr1 34611 36081 FAM138C

and 1) my resolution is not good ^^', 2) i can't get my genes names! do you have any ideas why? thanks!

Marine

hicPlotTADs --tracks hic_track2.ini -o test2.png --region chr7:156500000-160000000

INFO:pygenometracks.tracksClass:initialize 1. [x-axis] INFO:pygenometracks.tracksClass:initialize 2. [hic matrix] INFO:pygenometracks.tracksClass:initialize 3. [tads] 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2/2 [00:00<00:00, 4563.99it/s] INFO:pygenometracks.tracksClass:initialize 4. [Genes] 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1861/1861 [00:00<00:00, 66631.95it/s] INFO:pygenometracks.tracksClass:time initializing track(s): INFO:pygenometracks.tracksClass:10.641975164413452 DEBUG:pygenometracks.tracksClass:Figure size in cm is 40 x 17.631405255403056. Dpi is set to 72

INFO:pygenometracks.tracksClass:plotting 1. [x-axis] INFO:pygenometracks.tracksClass:plotting 2. [hic matrix] WARNING:pygenometracks.tracks.GenomeTrack:Warning The region to plot extends beyond the chromosome size. Please check. chr7 size: 159345973. Region to plot 156500000-160000000

INFO:pygenometracks.tracks.GenomeTrack:setting min, max values for track 2. [hic matrix] to: 5.0, 50.0

INFO:pygenometracks.tracksClass:plotting 3. [tads] INFO:pygenometracks.tracksClass:plotting 4. [Genes] DEBUG:pygenometracks.tracks.GenomeTrack:ylim 74.67999999999999,-0.08

[lldelisle]

Hi,

1. For the resolution, in the name of your h5 I read: '50000' so it might be 50kb, not 5kb.
2. For the gene_name, by default the labels are not printed if you have more than 60 genes. To change it, just increase the value: max_labels = 60. You can read more details on all parameters on gene tracks in our documentation.

Tell me if this solves your issues.