Assembly unable to align in Juicebox

Arushi Khanna

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Jun 30, 2021, 5:50:30 PM6/30/21

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Hi everyone,

We are able to visualize Hi-C data in Juicebox, but are unable to align the hg19.assembly file (attached below) onto it. Either the program goes into an infinite "loading..." screen or the assembly just does not show up. Should we cut off all the lines after ">MT 25 16569" in the assembly file?

Do you have any other suggestions?

Thank you so much!

Arushi Khanna

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Jul 1, 2021, 10:16:35 AM7/1/21

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Having issues attaching the assembly but here is the content:

>1 1 249250621

>2 2 243199373

>3 3 198022430

>4 4 191154276

>5 5 180915260

>6 6 171115067

>7 7 159138663

>8 8 146364022

>9 9 141213431

>10 10 135534747

>11 11 135006516

>12 12 133851895

>13 13 115169878

>14 14 107349540

>15 15 102531392

>16 16 90354753

>17 17 81195210

>18 18 78077248

>19 19 59128983

>20 20 63025520

>21 21 48129895

>22 22 51304566

>X 23 155270560

>Y 24 59373566

>MT 25 16569

>GL000207.1 26 4262

>GL000226.1 27 15008

>GL000229.1 28 19913

>GL000231.1 29 27386

>GL000210.1 30 27682

>GL000239.1 31 33824

>GL000235.1 32 34474

>GL000201.1 33 36148

>GL000247.1 34 36422

>GL000245.1 35 36651

>GL000197.1 36 37175

>GL000203.1 37 37498

>GL000246.1 38 38154

>GL000249.1 39 38502

>GL000196.1 40 38914

>GL000248.1 41 39786

>GL000244.1 42 39929

>GL000238.1 43 39939

>GL000202.1 44 40103

>GL000234.1 45 40531

>GL000232.1 46 40652

>GL000206.1 47 41001

>GL000240.1 48 41933

>GL000236.1 49 41934

>GL000241.1 50 42152

>GL000243.1 51 43341

>GL000242.1 52 43523

>GL000230.1 53 43691

>GL000237.1 54 45867

>GL000233.1 55 45941

>GL000204.1 56 81310

>GL000198.1 57 90085

>GL000208.1 58 92689

>GL000191.1 59 106433

>GL000227.1 60 128374

>GL000228.1 61 129120

>GL000214.1 62 137718

>GL000221.1 63 155397

>GL000209.1 64 159169

>GL000218.1 65 161147

>GL000220.1 66 161802

>GL000213.1 67 164239

>GL000211.1 68 166566

>GL000199.1 69 169874

>GL000217.1 70 172149

>GL000216.1 71 172294

>GL000215.1 72 172545

>GL000205.1 73 174588

>GL000219.1 74 179198

>GL000224.1 75 179693

>GL000223.1 76 180455

>GL000195.1 77 182896

>GL000212.1 78 186858

>GL000222.1 79 186861

>GL000200.1 80 187035

>GL000193.1 81 189789

>GL000194.1 82 191469

>GL000225.1 83 211173

>GL000192.1 84 547496

>NC_007605 85 171823

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Thanks so much!

Olga Dudchenko

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Jul 1, 2021, 11:16:15 AM7/1/21

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Hi Arushi,

The assembly file per se looks fine to me. Is your hic file JBAT-compatible? I.e. is it against the "assembly chromosome". If not/unsure, check page 5 of the Genome Assembly Cookbook.

Best,

Olga

Arushi Khanna

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Jul 2, 2021, 3:23:42 PM7/2/21

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Hi Olga,

Our Hi-C file (.hic) was generated through HiCPro and then converted to .hic on the back end (HiC-Pro/hicpro2juicebox.sh) - would that cause any differences or make the final .hic file not JBAT compatible?

Thanks!

Olga Dudchenko

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Jul 2, 2021, 5:04:55 PM7/2/21

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Sorry, I don't know anything about Hi-C pro. I doubt that it converts into a format compatible with JBAT though. -Olga

Berkley Gryder

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Jul 3, 2021, 12:25:12 PM7/3/21

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Olga, Arushi: I am going to try to rebuild the .hic files from the fasta using juicer tools, rather than HiCPro. It may be tricky since ours is MNase digested and has a linker that needs to be trimmed... we'll see how it goes.

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