search

robinweide / GENOVA

GENome Organisation Visual Analytics
GNU General Public License v3.0
68 stars 15 forks source link

Issue reading in .hic (possibly due to juicer hic version 9) #332

Closed tolender closed 1 year ago

tolender commented 1 year ago

Hi,

I am trying to read in my .hic but it seems to be looking at the wrong column for the resolution info in the hic file. My .hic files are juicer v9, could this be a file version error?

WT.hic.juicer <- load_contacts(signal_path = 'data/WT.hic', sample_name = "WT", resolution = 10000, balancing = "KR")

Reading data... Error in loadJuicer(juicerPath, resolution, scale_bp = scale_bp, scale_cis = scale_cis, : resolution is not found. Available resolutions are -1828132276, 1077797004, -1074584380, -888507814, -770413841, 616882835, 130615830, -1458951954, -1491534451, 585037374, 1563262033, 1504091578, 1281046761, 178777955, 756390227, 1266036046, 591981132, 1021326707, 1683382740, 389355327, 1001312454, 1870000005, 959597790, -446819100, -917928723, 639998438, 1233722003, 31038428, 649763874, -442309899, 172776144, -1491045099, -1718662778, -1889323078, 485349702, -438765196, -643450053, 761503998, -1827775980, -1734448848, -1146869662, -1164177838, 1611381013, -1738082546, -195665714, -1070239385, 1401198677, 1117556947, 934829419, 490186924, -975688088, -747292567, 1164347815, -1725871681, 1233242284, -978626327, 1173440907, 647173491, -215694181, 1164333772, -555655660, -456741674, 978509208, -1269401482, -382680713, 1721173436, -835043161, 558517295, 616795795, 386365842, 1619367022, 606630261, 956211133, -1590434796, 1593416006, -457941939, -884617557, -1903035757, 50080201, 1

teunbrand commented 1 year ago

I've never seen a v9 .hic file before, do you happen to know of some publicly available sample data to test solutions with?

tolender commented 1 year ago

It is related to the Juicer v2.x update, as v9 hic files have slightly different formatting than previous hic files in Juicer v1.x .

https://github.com/aidenlab/juicer/wiki/FAQs see Version issues (1.x vs 2.x)

teunbrand commented 1 year ago

Thanks for the link, I've assumed as much about the formatting. I don't know when I'll have time to debug this unfortunately.

tolender commented 1 year ago

Thanks for looking into it.

teunbrand commented 1 year ago

I'm going to keep this open as a reminder to look into it.

teunbrand commented 1 year ago

@tolender can I get you to try out the dev branch to see if this has solved the loading issue? You can install from the dev branch with devtools::install_github("robinweide/GENOVA", ref = "dev")

tolender commented 1 year ago

I installed the dev branch and I am now able to continue with the vignette, thank you so much!

teunbrand commented 1 year ago

Thanks for checking!