mESC Dixon

[Enrichetta Mileti]

Hi! 

I'm trying to use Juicer in mESC from Dixon et al 2012 with mm10. 

This is the command that I use:

$DIR_SCRIPTS/juicer.sh -g mm10 -S merge -d $DIR_DATA -z $DIR_SCRIPTS/references/mm10/Mus_musculus_assembly10.fasta -y $DIR_SCRIPTS/restriction_sites/mm10_HindIII.txt -D $DIR_SCRIPTS  -p $DIR_CHROM_SIZES

However, I got this error:

(-: Finished sorting all sorted files into a single merge.

Picked up _JAVA_OPTIONS: -Xmx16384m

Exception in thread "main" java.lang.UnsupportedClassVersionError: LibraryComplexity : Unsupported major.minor version 52.0

        at java.lang.ClassLoader.defineClass1(Native Method)

        at java.lang.ClassLoader.defineClass(ClassLoader.java:792)

        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)

        at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)

        at java.net.URLClassLoader.access$100(URLClassLoader.java:71)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:361)

        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

        at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

Picked up _JAVA_OPTIONS: -Xmx16384m

Start preprocess

Writing header

Writing body

..............................................................................................................................................................................................................................................................

Writing footer

Finished preprocess

Calculating norms for zoom BP_2500000

Calculating norms for zoom BP_1000000

Calculating norms for zoom BP_500000

Calculating norms for zoom BP_250000

Calculating norms for zoom BP_100000

Calculating norms for zoom BP_50000

Calculating norms for zoom BP_25000

Calculating norms for zoom BP_10000

Calculating norms for zoom BP_5000

Calculating norms for zoom FRAG_500

Calculating norms for zoom FRAG_200

Calculating norms for zoom FRAG_100

Calculating norms for zoom FRAG_50

Calculating norms for zoom FRAG_20

Calculating norms for zoom FRAG_5

Calculating norms for zoom FRAG_2

Calculating norms for zoom FRAG_1

Writing expected

Writing norms

Finished writing norms

In the final folder I have both .hic files but I don't understand what is going wrong.

Thanks for your help!

[Neva Durand]

This looks like a problem with different compiled versions of the LibraryComplexity class. You are probably missing that value in your statistics file. Double check but I imagine your hic files are fine. 

--
You received this message because you are subscribed to the Google Groups "3D Genomics" group.
To unsubscribe from this group and stop receiving emails from it, send an email to 3d-genomics...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/076d8909-b8b4-47d2-847a-fce73b84ae3e%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Enrichetta Mileti]

Hi Neva,

Thanks for your reply. This is how the stat file looks like:

Intra-fragment Reads: 2,282,198(32.19%)

Below MAPQ Threshold: 547,773(7.73%)

Hi-C Contacts: 4,259,277(60.08%)

 Ligation Motif Present: 343 (0.00%)

 3' Bias (Long Range): 90% - 10%

 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%

Inter-chromosomal: 539,164 (7.61%)

Intra-chromosomal: 3,720,113 (52.48%)

Short Range (<20Kb): 1,835,829 (25.90%)

Long Range (>20Kb): 1,884,277 (26.58%)

[Neva Durand]

Try loading the hic files into Juicebox 

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/07417cd9-48dc-4835-a73c-849b176dc991%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Enrichetta Mileti]

Hi again,

I loaded the file in JuiceBox and this is how they look like:

The order of the chromosomes is random (In the 3rd column I have X chromosome)

[Neva Durand]

That’s because your chrom.sizes file is in that order. 

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/f3de0435-ad4a-4260-af5a-906c07ff2962%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Enrichetta Mileti]

Ok fine.

what I was wondering is why I don't see any signal in Y chromosome (That is the grey column). In the data present in Juicebox there is signal.

[Neva Durand]

Is it in your data (in the merged nodups)? And has the same name as in the chrom sizes?

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/545c0091-4569-4a5c-b3bf-17b1afd8dde5%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.